Electrochemically removable protecting groups for DNA synthesis

Abstract

Described herein are compositions and methods for polynucleotide synthesis. The composition for synthesis can comprise a nucleoside; and at least one protecting group, wherein the protecting group is configured for electrochemical removal under mild conditions. Methods include extending a polynucleotide, wherein the polynucleotide is extended by deprotecting a first protected nucleotide to generate a deprotected nucleotide. Methods may further include contacting the deprotected nucleotide with a second protected nucleotide thereby extending the polynucleotide.

Description

Attorney Docket No. 00415-0062-00304PROTECTING GROUPS FOR DNA SYNTHESISCROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Patent Application No. 63 / 701,881, filed on October 01, 2024. which is hereby incorporated by reference in its entirety. All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.BRIEF SUMMARY

[0002] Provided herein are compositions for polynucleotide synthesis, comprising: (a) a nucleoside; and (b) at least one protecting group, wherein the protecting group is configured for electrochemical removal under mild conditions. In some instances, mild conditions comprises use of aqueous solvents. In some instances, mild conditions comprises use of less acid for deprotection than DMT. In some instances, the at least one protecting group is a 5’ protecting group on the nucleoside. In some instances, the at least one protecting group is a 3‘ protecting group on the nucleoside. In some instances, the composition comprises two protecting groups. In some instances, the at least one protecting group comprises an acid-cleavable protecting group. In some instances, the at least one protecting group comprises a base-cleavable protecting group. In some instances, the at least one protecting group is connected to a 5’ oxygen of the nucleoside by a nitrogen atom. In some instances, the composition comprises the structure:wherein B is an optionally protected nucleobase; R1and R2are independently selected at each occurrence from hydrogen, halogen, Ci-io alkyl, Ci-io heteroalkyl, -SR4, -N(R4)2, -N (R5). - C(O)R4, -C(O)OR4, -C(O)N(R4)2, -N(R4)C(O)R4, -N(R4)C(O)OR4, -N(R4)C(O)N(R4)2, - N(R4)C(S)N(R4)2, -N(R4)S(O)2(R4), -S(O)R4, -S(O)2R4, -S(O)2N(R4)2, -NO2, =S, -N=(R7), -CN, - P(O)(OR6)2, -P(O)R6(OR6), -P(OR6)N(R6)2, -S(O)2OR4, C3-10 carbocycle and 3- to 10-membered heterocycle, wherein the C1-10 alkyl. C 1-10 heteroalkyl. C3-10 carbocycle, or 3- to 10-membered heterocycle is optionally substituted with one or more substituents independently selected from halogen, -OR4, -SR4, -N(R4)2, -N+(R5)3, -C(O)OR4, -P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, - S(O)2R4, and =0; R3is selected from hydrogen, halogen, hydroxyl, C1-10 alkyl, C1-10 heteroalkyl, -SR4. -N(R4)2, -N (R5)3, -C(O)R4, -C(O)OR4, -OC(O)R4, -OC(O)N(R4)2, -C(O)N(R4)2. -Attorney Docket No. 00415-0062-00304N(R4)C(O)R4, -N(R4)C(O)OR4, -N(R4)C(O)N(R4)2. -N(R4)C(S)N(R4)2. -N(R4)S(O)2(R4). - S(O)R4, -S(O)2R4, -S(O)2N(R4)2, -NO2, =S, -N=(R7), -CN, -P(O)(OR6)2, -P(O)R6(OR6), - P(OR6)N(R6)2, -S(O)2OR4. C3-10 carbocycle and 3- to 10-membered heterocycle, wherein the Ci- 10 alkyl, Ci-10 heteroalkyl, C3-10 carbocycle, or 3- to 10-membered heterocycle is optionally substituted with one or more substituents independently selected from halogen. -OR4, -SR4, - N(R4)2, -N+(R5)3, -C(O)OR4, -P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, -S(O)2R4, and =0; R4is independently selected at each occurrence from hydrogen, C1-10 alkyl, and C1-10 heteroalkyl, wherein the C1-10 alkyl or C1-10 heteroalkyl is optionally substituted with one or more substituents independently selected from: halogen, -OR8, -SR8, -N(R8)2, -N+(R5)3. -C(O)OR8, -P(O)(OR6)2. - P(O)R6(OR6), -S(O)2OR6, -S(O)2R8, =0, and C3-10 carbocycle, wherein each C3-10 carbocycle is optionally substituted with one or more substituents independently selected from halogen, -OR8, C1-6 alkyd, C1-6 haloalkyl, C 1-6 hydroxy alk l, and =0; R5is independently selected at each occurrence from hydrogen and C1-4 alkyl; R6is independently selected at each occurrence from hydrogen, C1-6 alkyd, and -CN; R7is selected from C3-10 carbocycle and 3- to 10-membered heterocycle, wherein each C3-10 carbocycle and 3- to 10-membered heterocycle is optionally substituted with one or more substituents independently selected from -OH, C1-6 alkyl, C1-6 haloalkyl, C1-6 hydroxyalkyl, and =0; and R8is selected from hydrogen and C1-4 alkyd. In some instances, R1or R2is -N(R4)2, -N(R7), -P(OR6)N(R6)2. or C1-10 alkyl. In some instances. R1or R2comprise a mono, di, tri, or polyphosphate. In some instances, R4is independently selected at each occurrence from hydrogen and C1-10 alkyl. In some instances, the C1-10 alkyl is substituted with one or more substituents, wherein the one or more substituents is a C3-10 carbocycle. In some instances, the C3-10 carbocycle substituted with -OR8. In some instances, R8is a Ci-4 alkyl.In some instances, R1or R2has the structure:In some instances, R7is a C3-10 carbocycle. In some instances, the C3-10 carbocycle is substituted with =0. In some instances, R1or R2has the structure:. In some instances, R6is independently selected at each occurrence from C1-6 alkyd and -CN. In some instances, R1or R2has the structure:Attorney Docket No. 00415-0062-00304. In some instances, the Ci-io alkyl is substituted with -OR4. In some instances,R4is a Ci-io alky l. In some instances, R1or R2has the structure: . In some instances, the composition comprises the structure:In some instances, the composition comprises the structure:Attorney Docket No. 00415-0062-00304instances, the composition comprises the structure:Attorney Docket No. 00415-0062-00304. In some instances, whenR1is hydrogen, R2is not hydrogen. In some instances, when R2is hydrogen, R1is not hydrogen.

[0003] Also provided herein are polynucleotides comprising the composition described herein. In some instances, the composition is attached to the 5’ terminus of the polynucleotide. In some instances, the composition is attached to the 3’ terminus of the polynucleotide.

[0004] Further provided herein are methods for polynucleotide synthesis comprising extending a polynucleotide, wherein the polynucleotide is extended by: (a) deprotecting a first protected nucleotide to generate a deprotected nucleoside; wherein the first protected nucleotide comprises the composition described herein. In some instances, the method further comprises: (b) contacting the deprotected nucleotide with a second protected nucleotide thereby extending the polynucleotide; and (c) repeating (a)-(b) to synthesize the polynucleotide. In some instances, the second protected nucleotide comprises the composition described herein. In some instances, the deprotecting comprises exposing the first protected nucleotide or the second protected nucleotide to a solvent. In some instances, deprotecting the first protected nucleotide or the second protected nucleotide comprises applying a voltage. In some instances, applying the voltage comprises reductive deblocking. In some instances, the voltage is about -1 V to about -2 V. In some instances, the voltage is about -1.3V to about -1.9V. In some instances, the deprotection comprises a deprotection efficiency of at least 85%. In some instances, applying the voltage comprise generating acid. In some instances, the acid is generated by the solvent in fluid communication with the first protected nucleotide. In some instances, the voltage is applied for about 50 seconds. In some instances, the deprotection comprises a deprotection efficiency of at least 87%. In some instances, the deprotection comprises a deprotection efficiency of at least 95%. In some instances, the deprotection comprises a deprotection efficiency of at least 97%. In some instances, the deprotection comprises a deprotection efficiency of at least 99%. In some instances, contacting comprises coupling the second protected nucleotide to the deprotected nucleotide. In some instances, the second protected nucleotide and the deprotected nucleotide are coupled via phosphorami di te synthesis or enzymatic synthesis. In some instances, the polynucleotide is attached to a solid support. In some instances, the first protected nucleotide is attached to the solid support. In some instances, the solid support comprises an addressableAttorney Docket No. 00415-0062-00304 surface. In some instances, the solid support comprises a CMOS chip. In some instances, the solid support comprises one or more active areas for polynucleotide synthesis. In some instances, the one or more active areas have a pitch distances of about 1 um. In some instances, the one or more active areas have a pitch distances of about 2 um.BRIEF DESCRIPTION OF THE DRAWINGS

[0005] A better understanding of the features and advantages of the present subject matter will be obtained by reference to the following detailed description that sets forth illustrative embodiments and the accompanying drawings of which:

[0006] FIGs. 1A-1C show a non-limiting example of oligonucleotides structures with protecting groups, according to some embodiments. FIG. 1A depicts the structure of a DMT-protected oligo. FIG. IB depicts the structure of an aminoxyl-protected oligo. FIG. 1C depicts a DMT- aminoxyl-protected oligo.

[0007] FIG. 2 shows a non-limiting example of a proposed mechanism of DMT-aminooxyl deblocking, according to some embodiments.

[0008] FIG. 3 shows a non-limiting example of a surrogate phosphoramidite, according to some embodiments.

[0009] FIG. 4 shows LCMS results of deblocking and coupling of various amidites, according to some embodiments. FIG. 4, from top to bottom, shows results for the following amidites: A, C, G, T, as well as no deblocking, respectively.

[0010] FIGs. 5A-5B show non-limiting examples of oligonucleotides structures with one or more protecting groups, according to some embodiments. FIG. 5A depicts the structure of a 3' ketal protected phosphoramidite. FIG. 5B depicts the structure of 5’ iminoxy protected phosphoramidite.[Oi l] FIG. 6 shows a non-limiting example of a proposed quinone oxime protected DNA synthesis process, according to some embodiments.

[0012] FIGs. 7A-7B show a non-limiting example of a proposed phosphoramidite chemical deblocking using dithiothreitol (DTT), according to some embodiments. FIG. 7A depicts a mechanism comprising initial protonation at the nitrogen of the iminoxy group, while FIG. 7B depicts a mechanism comprising initial protonation at the quinone ketone.

[0013] FIG. 8 shows LCMS results from exposure of a 5’-oxime protected poly-deoxythymdine (dT) with DTT, according to some embodiments. FIG. 8, from top to bottom, shows results for TIO-T-oxime, TIO-T-oxime and DTT deblocking, and TIO-T-oxime, DTT deblocking, dAAttorney Docket No. 00415-0062-00304 coupling and oxidation, respectively.

[0014] FIGs. 9A-9B show a non-limiting example of a proposed phosphoramidite chemical deblocking using methyl blue (MB), according to some embodiments. FIG. 9A depicts cathodic reduction of an electronic deblock auxiliary reagent (methylene blue). Without being bound by theory, FIG. 9B depicts a mechanism of iminoxy quinone deprotection using methylene blue.

[0015] FIGs. 10A-10B show LCMS results of deblocking and coupling of 5 ’-oxime protected amidites, according to some embodiments. FIG. 10A provides LCMS results at -1.3 V, -1.6V, - 1.9V, -2.2 V, and 0V, from top to bottom, respectively. FIG. 10B provides LCMS results at - 2.2V. -2.5V, -2.8V, -3.1V. and 0V, from top to bottom, respectively.

[0016] FIGs. 11A-11B show microscope images of the oxime deblocking confined within the active area in lum (FIG. 11A) and 2 urn (FIG. 11B) pitch apart, according to some embodiments.

[0017] FIG. 12 shows a table with details of the subroutine for electrochemical deblocking, according to some embodiments.

[0018] FIGs. 13A-13B shows mass spectroscopy results from electrochemical deblocking, according to some embodiments. FIG. 13A provides LCMS results at -2.1V, -1.9V, and 0V, from top to bottom, respectively. FIG. 13B depicts an expanded inset for LCMS results at - 1.9V.

[0019] FIGs. 14A-14F illustrates views of an exemplary high density device for polynucleotide synthesis, according to some embodiments. FIG. 14A illustrates a cross-section view of a high- density device for polynucleotide synthesis. Two exemplary addressable device arrays are shown for clan ty only. FIG. 14B illustrates a top view of a high-density device for polynucleotide synthesis. Nine exemplary addressable device arrays are shown for clarity only. FIG. 14C illustrates a top view of a high-density device for polynucleotide synthesis. Four exemplary addressable device arrays are shown for clarity only. FIG. 14D illustrates a cross-section view of a high-density device for polynucleotide synthesis. Two exemplary device arrays are shown for clarity only. FIG. 14E illustrates a top view of a high-density device for polynucleotide synthesis. Sixteen exemplary addressable device arrays are shown for clarity only. FIG. 14F illustrates a cross-section view7of a high-density’ device for polynucleotide synthesis, comprising a device layer for polynucleotide synthesis in communication with a CMOS chip.

[0020] FIGs. 15A-15D illustrate a computer system, according to some embodiments. FIG. 15A illustrates a non-limiting example of a computer system. FIG. 15B illustrates a block diagram illustrating architecture of a computer system. FIG. 15C illustrates diagram demonstrating a netw ork configured to incorporate a plurality of computer systems, a pluralityAttorney Docket No. 00415-0062-00304 of cell phones and personal data assistants, and Network Attached Storage (NAS). FIG. 15D illustrates a block diagram of a multiprocessor computer system using a shared virtual address memory space.

[0021] FIG. 16 illustrates a reaction scheme for DNA synthesis, according to some embodiments.DETAILED DESCRIPTION

[0022] Provided herein are protecting groups for DNA synthesis. Conventional dimethoxytrityl (DMT) protected phosphoramidites can require harsh acidic conditions to remove the protecting group. However, aminnooxyl protected phosphoramidites can show high lability and may have difficulty surviving in certain aqueous electrochemical processes. Provided herein are synthesis strategies utilizing a DMT-aminooxyl protected amidites to overcome such problems. The protecting groups may be used in aqueous (rather than organic solvent based) electrochemical deblocking methods, and introduce an environmentally benign pathway. In some instances, the protecting groups may be used in enzymatic DNA synthesis due its compatibility with bioactive proteins.

[0023] Further provided herein are methods and compositions for usage of quinone oxime protected nucleotides which can provide a milder deblocking pathway for DNA synthesis compared to a conventional DMT deblocking process. Quinone oxime can be stable and compatible with versatile conditions. Further, electrochemical deblocking of such a protecting group may be performed in aqueous solution. However, previous aqueous electrochemical deblocking progress, such as 3’ or 5’-aminooxyl oligonucleotide deprotection, may be labile and interact with aqueous electrochemical deblocking solution, nucleotide units, or enzymes, and thus there may be further optimization of chemical or enzymatic synthesis of oligos.

[0024] Provided herein are compositions for polynucleotide synthesis. A composition for polynucleotide synthesis can comprise a nucleoside and at least one protecting group. In some instances, the protecting group is configured for electrochemical removal.

[0025] Also provided herein are methods for polynucleotide synthesis comprising extending a polynucleotide. In some instances, the polynucleotide is extended by (a) deprotecting a first protected nucleotide to generate a deprotected nucleotide. In some examples, the first protected nucleotide comprises a composition described herein.

[0026] Definitions

[0027] Throughout this disclosure, various embodiments are presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of any embodiments.Attorney Docket No. 00415-0062-00304Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range to the tenth of the unit of the lower limit unless the context clearly dictates otherwise. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4. from 2 to 6, from 3 to 6 etc., as well as individual values within that range, for example, 1.1, 2, 2.3, 5, and 5.9. This applies regardless of the breadth of the range. The upper and lower limits of these intervening ranges may independently be included in the smaller ranges, and are also encompassed within the disclosure, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the disclosure, unless the context clearly dictates otherwise.

[0028] The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of any embodiment. As used herein, the singular forms “a,” “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms “comprises” and / or “comprising,” when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and / or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and / or groups thereof. As used herein, the term “and / or” includes any and all combinations of one or more of the associated listed items.

[0029] Unless specifically stated or obvious from context, as used herein, the term “about” in reference to a number or range of numbers is understood to mean the stated number and numbers + / - 10% thereof, or 10% below the lower listed limit and 10% above the higher listed limit for the values listed for a range.

[0030] Unless specifically stated, as used herein, the term “nucleic acid” encompasses double- or triple-stranded nucleic acids, as well as single-stranded molecules. In double- or triplestranded nucleic acids, the nucleic acid strands need not be coextensive (i. e. , a double-stranded nucleic acid need not be double-stranded along the entire length of both strands). Nucleic acid sequences, when provided, are listed in the 5’ to 3’ direction, unless stated otherwise. Methods described herein provide for the generation of isolated nucleic acids. Methods described herein additionally provide for the generation of isolated and purified nucleic acids. A “nucleic acid” as referred to herein can comprise at least 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, or more bases in length.Attorney Docket No. 00415-0062-00304Moreover, provided herein are methods for the synthesis of any number of polypeptide-segments encoding nucleotide sequences, including sequences encoding non-ribosomal peptides (NRPs), sequences encoding non-ribosomal peptide-synthetase (NRPS) modules and synthetic variants, polypeptide segments of other modular proteins, such as antibodies, polypeptide segments from other protein families, including non-coding DNA or RNA. such as regulatory sequences e.g. promoters, transcription factors, enhancers, siRNA, shRNA, RNAi, miRNA, small nucleolar RNA derived from microRNA, or any functional or structural DNA or RNA unit of interest. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, intergenic DNA. loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), small nucleolar RNA, ribozymes, complementary DNA (cDNA), which is a DNA representation of mRNA, usually obtained by reverse transcription of messenger RNA (mRNA) or by amplification; DNA molecules produced synthetically or by amplification, genomic DNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. cDNA encoding for a gene or gene fragment referred herein may comprise at least one region encoding for exon sequences without an intervening intron sequence in the genomic equivalent sequence. cDNA described herein may be generated by de novo synthesis.

[0031] Provided herein are methods and compositions for production of polynucleotides. Polynucleotides may also be referred to as oligonucleotides or oligos.

[0032] "Amino" refers to the -NH2 radical.

[0033] "Cyano" refers to the CN radical.

[0034] "Nitro" refers to the NO2 radical.

[0035] "Oxa" refers to the -O- radical.

[0036] "Oxo" refers to the =0 radical.

[0037] "Thioxo" refers to the =S radical.

[0038] "Imino" refers to the =N-H radical.

[0039] "Oximo" refers to the =N-0H radical.

[0040] "Hydrazine" refers to the =N-NH2 radical.

[0041] "Alkyl" refers to a straight or branched hydrocarbon chain radical consisting solely of carbon and hydrogen atoms, containing no unsaturation, having from one to fifteen carbon atoms (e.g., Cl -Cl 5 alkyl). In certain embodiments, an alkyl comprises one to thirteen carbon atoms (e.g., C1-C13 alkyl). In certain embodiments, an alkyl comprises one to eight carbon atoms (e.g.,Attorney Docket No. 00415-0062-00304C1-C8 alkyl). In other embodiments, an alkyl compnses one to five carbon atoms (e.g., C1-C5 alkyl). In other embodiments, an alkyl comprises one to four carbon atoms (e.g., C1-C4 alkyl). In other embodiments, an alky l comprises one to three carbon atoms (e.g., C1-C3 alkyl). In other embodiments, an alkyl comprises one to two carbon atoms (e.g., C1-C2 alkyl). In other embodiments, an alkyl comprises one carbon atom (e.g., Cl alkyl). In other embodiments, an alkyl comprises five to fifteen carbon atoms (e g., C5-C 15 alkyl). In other embodiments, an alkyl comprises five to eight carbon atoms (e.g., C5-C8 alkyl). In other embodiments, an alkyl comprises two to five carbon atoms (e.g., C2-C5 alkyl). In other embodiments, an alkyl comprises three to five carbon atoms (e.g., C3-C5 alkyl). In other embodiments, the alkyl group is selected from methyl, ethyl, 1 propyl (n-propyl), 1 -methylethyl (iso propyl), 1 -butyl (n butyl), 1 -methylpropyl (sec-butyl), 2-methylpropyl (iso-butyl), 1,1 dimethylethyl (tert butyl), 1 pentyl (n-pentyl). The alkyl is attached to the rest of the molecule by a single bond. Unless stated otherwise specifically in the specification, an alkyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo. trimethylsilanyl, -ORa, -SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra, -C(O)ORa, -C(O)N(Ra)2, - N(Ra)C(O)ORa, -OC(O)-N(Ra)2, -N(Ra)C(O)Ra, -N(Ra)S(O)tRa (where t is 1 or 2), -S(O)tORa (where t is 1 or 2), -S(O)tRa (where t is 1 or 2) and S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), ary l (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).

[0042] "Alkoxy" refers to a radical bonded through an oxygen atom of the formula -O-alkyl, where alkyl is an alkyl chain as defined above.

[0043] "Alkenyl" refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one carbon-carbon double bond, and having from two to twelve carbon atoms. In certain embodiments, an alkenyl comprises two to eight carbon atoms. In other embodiments, an alkenyl comprises two to four carbon atoms. The alkenyl is attached to the rest of the molecule by a single bond, for example, ethenyl (i.e., vinyl),Attorney Docket No. 00415-0062-00304 prop 1 enyl (i.e.. allyl), but 1 enyl. pent 1 enyl, penta 1,4 dienyl, and the like. Unless stated otherwise specifically in the specification, an alkenyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -ORa, -SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra, -C(O)ORa, -C(O)N(Ra)2, - N(Ra)C(O)ORa, -OC(O)-N(Ra)2, -N(Ra)C(O)Ra. -N(Ra)S(O)tRa (where t is 1 or 2), -S(O)tORa (where t is 1 or 2), -S(O)tRa (where t is 1 or 2) and -S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy , or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).

[0044] "Alkynyl" refers to a straight or branched hydrocarbon chain radical group consisting solely of carbon and hydrogen atoms, containing at least one carbon-carbon triple bond, having from two to twelve carbon atoms. In certain embodiments, an alkynyl comprises two to eight carbon atoms. In other embodiments, an alkynyl comprises two to six carbon atoms. In other embodiments, an alky nyl comprises two to four carbon atoms. The alkynyl is attached to the rest of the molecule by a single bond, for example, ethynyl, propynyl. butynyl, pentynyl, hexynyl, and the like. Unless stated otherwise specifically in the specification, an alkynyl group is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -ORa, -SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra, -C(O)ORa, -C(O)N(Ra)2, -N(Ra)C(O)ORa, -OC(O)-N(Ra)2, -N(Ra)C(O)Ra, -N(Ra)S(O)tRa (where t is 1 or 2). -S(O)tORa (where t is 1 or 2). -S(O)tRa (where t is 1 or 2) and S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted wi th halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethy l), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy,Attorney Docket No. 00415-0062-00304 methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).

[0045] "Alkylene" or "alkylene chain" refers to a straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group, consisting solely of carbon and hydrogen, containing no unsaturation and having from one to twelve carbon atoms, for example, methylene, ethylene, propylene, n butylene, and the like. The alkylene chain is attached to the rest of the molecule through a single bond and to the radical group through a single bond. The points of attachment of the alkylene chain to the rest of the molecule and to the radical group are through one carbon in the alkylene chain or through any two carbons within the chain. In certain embodiments, an alkylene comprises one to eight carbon atoms (e.g., C1-C8 alkylene). In other embodiments, an alkylene comprises one to five carbon atoms (e.g., C1-C5 alkylene). In other embodiments, an alkylene comprises one to four carbon atoms (e.g., C1-C4 alkylene). In other embodiments, an alkylene comprises one to three carbon atoms (e.g.. C1-C3 alkylene). In other embodiments, an alkylene comprises one to two carbon atoms (e.g., C1-C2 alkylene). In other embodiments, an alkydene comprises one carbon atom (e.g., Cl alkydene). In other embodiments, an alkylene comprises five to eight carbon atoms (e.g., C5-C8 alky lene). In other embodiments, an alkylene comprises two to five carbon atoms (e.g., C2-C5 alkylene). In other embodiments, an alkylene comprises three to five carbon atoms (e.g., C3-C5 alkylene). Unless stated otherwise specifically in the specification, an alkylene chain is optionally substituted by one or more of the following substituents: halo, cyano, nitro, oxo, thioxo, imino, oximo, trimethylsilanyl, -ORa, -SRa, -OC(O)-Ra, -N(Ra)2, -C(O)Ra. -C(O)ORa, -C(O)N(Ra)2, - N(Ra)C(O)ORa. -OC(O)- N(Ra)2. -N(Ra)C(O)Ra, -N(Ra)S(O)tRa (where t is 1 or 2), - S(O)tORa (where t is 1 or 2), -S(O)tRa (where t is 1 or 2) and -S(O)tN(Ra)2 (where t is 1 or 2) where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, carbocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), carbocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl).Attorney Docket No. 00415-0062-00304

[0046] "Aryl" refers to a radical derived from an aromatic monocyclic or multicyclic hydrocarbon ring system by removing a hydrogen atom from a ring carbon atom. The aromatic monocyclic or multicyclic hydrocarbon ring system contains only hydrogen and carbon from five to eighteen carbon atoms, where at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) 7T-electron system in accordance with the Hiickel theory. The ring system from which aryl groups are derived include, but are not limited to, groups such as benzene, fluorene, indane, indene, tetralin and naphthalene. Unless stated otherwise specifically in the specification, the term "ary l" or the prefix "ar " (such as in "aralkyl") is meant to include aryl radicals optionally substituted by one or more substituents independently selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb-ORa. -Rb-OC(O)-Ra, -Rb- OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, -Rb-C(O)Ra, -Rb-C(O)ORa, -Rb-C(O)N(Ra)2, - Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb-N(Ra)C(O)Ra, -Rb-N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), c cloalky I alky I (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), hcteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.

[0047] "Aralkyl" refers to a radical of the formula Rc ar l where Rc is an alkylene chain as defined above, for example, methylene, ethylene, and the like. The alkylene chain part of the aralkyl radical is optionally substituted as described above for an alkylene chain. The aryl part of the aralkyl radical is optionally substituted as described above for an aryl group.

[0048] "Carbocyclyl" or “cycloalkyl” refers to a stable non aromatic monocyclic or polycy clicAttorney Docket No. 00415-0062-00304 hydrocarbon radical consisting solely of carbon and hydrogen atoms, which includes fused or bridged ring systems, having from three to fifteen carbon atoms. In certain embodiments, a carbocyclyl comprises three to ten carbon atoms. In other embodiments, a carbocyclyl comprises five to seven carbon atoms. The carbocyclyl is attached to the rest of the molecule by a single bond. Carbocyclyl is saturated (i.e. , containing single C-C bonds only) or unsaturated (i.e.. containing one or more double bonds or triple bonds). A fully saturated carbocyclyl radical is also referred to as "cycloalkyl." Examples of monocyclic cycloalkyls include, e.g., cyclopropyl, cyclobutyl, cyclopenty l, cyclohexyl, cyclohepty l, and cyclooctyl. An unsaturated carbocycly l is also referred to as "cycloalkenyl." Examples of monocyclic cycloalkenyls include, e.g., cyclopentenyl, cyclohexenyl, cycloheptenyl, and cyclooctenyl. Polycyclic carbocyclyl radicals include, for example, adamantyl, norbomyl (i.e., bicyclo[2.2.1]heptanyl), norbomenyl, decalinyl, 7,7 dimethyl bicyclo[2.2.1]heptanyl, and the like. Unless otherwise stated specifically in the specification, the term "carbocyclyl" is meant to include carbocyclyl radicals that are optionally substituted by one or more substituents independently selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, oxo, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl. optionally substituted heteroaryl, optionally substituted heteroarylalkyl, Rb-ORa, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, - Rb-C(O)Ra, -Rb-C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, - Rb-N(Ra)C(O)Ra, -Rb-N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb- S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.Attorney Docket No. 00415-0062-00304

[0049] "Carbocyclylalkyl" refers to a radical of the formula -Rc carbocyclyl where Rc is an alkylene chain as defined above. The alkylene chain and the carbocyclyl radical are optionally substituted as defined above.

[0050] "Halo" or "halogen" refers to bromo, chloro, fluoro or iodo substituents.

[0051] "Fluoroalkyl" refers to an alkyl radical, as defined above, that is substituted by one or more fluoro radicals, as defined above, for example, trifluoromethyl, difluoromethyl, fluoromethyl, 2,2,2 trifluoroethyl, 1 fluoromethyl 2 fluoroethyl, and the like. In some embodiments, the alkyl part of the fluoroalkyl radical is optionally substituted as defined above for an alkyl group.

[0052] "Heterocyclyl" or “heterocycloalkyU refers to a stable 3 to 18 membered non-aromatic ring radical that comprises two to twelve carbon atoms and from one to six heteroatoms selected from nitrogen, oxygen and sulfur. Unless stated otherwise specifically in the specification, the heterocyclyl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which optionally includes fused or bridged ring systems. The heteroatoms in the heterocyclyl radical are optionally oxidized. One or more nitrogen atoms, if present, are optionally quatemized. The heterocyclyl radical is partially or fully saturated. The heterocyclyl is attached to the rest of the molecule through any atom of the ring(s). Examples of such heterocyclyl radicals include, but are not limited to, dioxolanyl, thienyl[l,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyL isoxazolidinyl, morpholinyL octahydroindolyl, octahydroisoindolyl, 2 oxopiperazinyl, 2 oxopiperidinyl, 2 oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4 piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1 oxo thiomorpholinyl. and 1,1 dioxo thiomorpholinyl. Unless stated otherwise specifically in the specification, the term "heterocyclyl" is meant to include heterocyclyl radicals as defined above that are optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, thioxo. cyano, nitro, optionally substituted and. optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb-ORa, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, - Rb-C(O)Ra, -Rb-C(O)ORa, -Rb-C(O)N(Ra)2. -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, - Rb-N(Ra)C(O)Ra, -Rb-N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb- S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, orAttorney Docket No. 00415-0062-00304 trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralky l (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.

[0053] "N-heterocyclyl" or “N-attached heterocyclyl” refers to a heterocyclyl radical as defined above containing at least one nitrogen and where the point of attachment of the heterocyclyl radical to the rest of the molecule is through a nitrogen atom in the heterocyclyl radical. An N heterocyclyl radical is optionally substituted as described above for heterocyclyl radicals. Examples of such N-heterocyclyl radicals include, but are not limited to, 1-morpholinyl, 1- piperidinyl, 1-piperazinyl, 1-pyrrolidinyl, pyrazolidinyl, imidazolinyl, and imidazolidinyl.

[0054] "C-heterocyclyl" or ’C-attached heterocyclyl” refers to a heterocyclyl radical as defined above containing at least one heteroatom and where the point of attachment of the heterocyclyl radical to the rest of the molecule is through a carbon atom in the heterocyclyl radical. A C heterocyclyl radical is optionally substituted as described above for heterocyclyl radicals. Examples of such C-heterocyclyl radicals include, but are not limited to, 2-morpholinyl, 2- or 3- or 4-piperidinyl, 2-piperazinyl, 2- or 3-pyrrolidinyL and the like.

[0055] "Heteroaryl" refers to a radical derived from a 3 to 18 membered aromatic ring radical that comprises two to seventeen carbon atoms and from one to six heteroatoms selected from nitrogen, oxygen and sulfur. As used herein, the heteroaryl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, wherein at least one of the rings in the ring system is fully unsaturated, i.e., it contains a cyclic, delocalized (4n+2) 7T-electron system in accordance with the Hiickel theory. Heteroaryl includes fused or bridged ring systems. The heteroatom(s) in the heteroaryl radical is optionally oxidized. One or more nitrogen atoms, if present, are optionally quatemized. The heteroaryl is attached to the rest of the molecule through any atom of the ring(s). Examples of heteroaryls include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzindolyl, 1,3 benzodi oxolyl, benzofuranyl, benzooxazolyl, benzo[d]thiazolyl, benzothiadiazolyl, benzo[b][l,4]dioxepinyl, benzo [b] [1,4] oxazinyl, 1,4Attorney Docket No. 00415-0062-00304 benzodioxanyl, benzonaphthofuranyl. benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl), benzothieno[3,2 d]pyrimidinyl, benzotriazolyl, benzo[4,6]imidazo[l,2 a]pyridinyl, carbazolyl, cinnolinyl, cyclopenta[d]pyrimidinyl, 6,7 dihydro 5H cyclopenta[4.5]thieno[2,3 d]pyrimidinyl, 5,6 dihydrobenzo[h]quinazolinyl, 5,6 dihydrobenzo[h]cinnolinyl. 6,7-dihydro-5H- benzo[6,7]cyclohepta[l,2-c]pyridazinyl, dibenzofuranyl, dibenzothiophenyl, furanyl, furanonyl, furo[3,2 c]pyridinyl, 5,6,7,8,9,10 hexahydrocycloocta[d]pyrimidinyl, 5,6,7,8,9,10 hexahydrocycloocta[d]pyridazinyl, 5,6,7,8,9,10 hexahydrocycloocta[d]pyridinyl, isothiazolyl, imidazolyl, indazolyl, indolyl, indazolyl, isoindolyl. indolinyl, isoindolinyl, isoquinolyl, indolizinyl, isoxazolyl, 5,8 methano 5,6,7,8 tetrahydroquinazolinyl, naphthyridinyl, 1,6 naphthyridinonyl, oxadiazolyl, 2 oxoazepinyl, oxazolyl, oxiranyl, 5,6,6a,7,8,9,10,10a octahydrobenzo[h]quinazolinyl, 1 phenyl 1H pyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl, pteridinyl, purinyl, pyrrolyl, pyrazolyl, pyrazolo[3,4 d]pyrimidinyl, pyridinyl, pyrido[3,2 d]pyrimidinyl. pyrido[3.4 d]pyrimidinyl, pyrazinyl. pyrimidinyl, pyridazinyl, pyrrolyl, quinazolinyl, quinoxalinyl, quinolinyl, isoquinolinyl, tetrahydroquinolinyl, 5, 6, 7, 8 tetrahydroquinazolinyl, 5, 6, 7, 8 tetrahydrobenzo[4,5]thieno[2,3 d]pyrimidinyl, 6, 7, 8, 9 tetrahydro 5H cyclohepta[4,5]thieno[2,3 d] pyrimidinyl, 5, 6, 7, 8 tetrahydropyrido[4,5 c] pyridazinyl, thiazolyl, thiadiazolyl, triazolyl, tetrazolyl, triazinyl, thieno[2,3 d]pyrimidinyl, thieno[3,2 d]pyrimidinyl, thieno[2,3 c]pyridinyl, and thiophenyl (i.e. thienyl). Unless stated otherwise specifically in the specification, the term "heteroaryl" is meant to include heteroaryl radicals as defined above which are optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, haloalkenyl, haloalkynyl, oxo, thioxo. cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb-ORa, -Rb-OC(O)- Ra. -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, -Rb-C(O)Ra, -Rb-C(O)ORa, -Rb- C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb-N(Ra)C(O)Ra, -Rb- N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyd, cycloalky 1 (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralky l (optionallyAttorney Docket No. 00415-0062-00304 substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaiy l (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Rc is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated.

[0056] "N-heteroaryl" refers to a heteroaryl radical as defined above containing at least one nitrogen and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a nitrogen atom in the heteroaiy l radical. An N-heteroaryl radical is optionally7substituted as described above for heteroaiy l radicals.

[0057] "C-heteroaryl" refers to a heteroaryl radical as defined above and where the point of attachment of the heteroaryl radical to the rest of the molecule is through a carbon atom in the heteroaryl radical. A C-heteroaryl radical is optionally substituted as described above for heteroaryl radicals.

[0058] The compounds disclosed herein, in some embodiments, contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric forms that are defined, in terms of absolute stereochemistry, as (R) or (S) . Unless stated otherwise, it is intended that all stereoisomeric forms of the compounds disclosed herein are contemplated by this disclosure. When the compounds described herein contain alkene double bonds, and unless specified otherwise, it is intended that this disclosure includes both E and Z geometric isomers (e.g.. cis or trans.) Likewise, all possible isomers, as well as their racemic and optically pure forms, and all tautomeric forms are also intended to be included. The term "‘geometric isomer” refers to E or Z geometric isomers (e.g., cis or trans) of an alkene double bond. The term “positional isomer” refers to structural isomers around a central ring, such as ortho-, meta-, and para- isomers around a benzene ring.

[0059] Compositions and Methods for Polynucleotide synthesis

[0060] Provided herein are compositions and methods for nucleic acid storage and synthesis. Synthesis or storage may, in some instances, be performed on solid supports. In some instances, solid supports comprise one or more surfaces. The one or more surfaces can comprise active regions for synthesis. Further provided herein are pluralities of devices which are combined to form larger arrays or chips. Further provided herein are devices and methods which are configured for electrochemical deprotection or deblocking during polynucleotide synthesis.Attorney Docket No. 00415-0062-00304Further provided herein are compositions comprising protecting groups suitable for electrochemical removal under milder conditions compared to conventional protecting groups (e.g., DMT). Further provided herein are methods which minimize voltages required for deblocking. Further provided herein are methods and compositions, including protecting groups, for aqueous electrochemical deblocking.

[0061] Compositions for polynucleotide synthesis can comprise a nucleoside or at least one protecting group. In some instances, the synthesis is phosphoramidite synthesis, electrochemical synthesis, or enzy matic synthesis. In some instances, the at least one protecting is configured for removal according to the synthesis method. In some examples, the protecting group is configured for electrochemical removal. In some examples, the at least one protecting group comprises an acid-cleavale protecting group or a base-cleavable protecting group. In some instances, the at least one protecting group is a 5’ protecting group on the nucleoside or a 3’ protecting group on the nucleoside. In some instances, the composition comprises two protecting groups.

[0062] Described herein are compositions comprising one or more protecting groups for DNA synthesis. In some instances, the composition comprises the structure:, whereinB is an optionally protected nucleobase. In some instances, R1and R2are independently selected at each occurrence from hydrogen, halogen. C1-10 alkyl, C1-10 heteroalkyl. -SR4. -N(R4)2, - N+(R5)3, -C(O)R4, -C(O)OR4, -C(O)N(R4)2, -N(R4)C(O)R4, -N(R4)C(O)OR4, -N(R4)C(O)N(R4)2, -N(R4)C(S)N(R4)2, -N(R4)S(O)2(R4), -S(O)R4, -S(O)2R4, -S(O)2N(R4)2, -NO2, =S, -N=(R7), -CN, -P(O)(OR6)2, -P(O)R6(OR6), -P(OR6)N(R6)2, -S(O)2OR4, C3-10 carbocycle and 3- to 10- membered heterocycle. In some examples, the C1-10 alkyl. C1-10 heteroalkyl, C3-10 carbocycle, or3- to 10-membered heterocycle is optionally substituted with one or more substituents independently selected from halogen, -OR4, -SR4, -N(R4)2, -N+(R5)3, -C(O)OR4, -P(O)(OR6)2, - P(O)R6(OR6), -S(O)2OR6, -S(O)2R4, and =0. In some instances, R3is selected from hydrogen, halogen, hydroxyl, Ci-io alkyl, Ci-io heteroalkyl, -SR4, -N(R4)2, -N+(R5)3, -C(O)R4, -C(O)OR4, - OC(O)R4, -OC(O)N(R4)2, -C(O)N(R4)2, -N(R4)C(O)R4. -N(R4)C(O)OR4. -N(R4)C(O)N(R4)2, - N(R4)C(S)N(R4)2, -N(R4)S(O)2(R4), -S(O)R4, -S(O)2R4, -S(O)2N(R4)2, -NO2, =S, -N=(R7), -CN, - P(O)(OR6)2, -P(O)R6(OR6), -P(OR6)N(R6)2, -S(O)2OR4, C3-10 carbocycle and 3- to 10-membered heterocycle. In some examples, the C1-10 alky l, C1-10 heteroalkyl, C3-10 carbocycle, or 3- to 10- membered heterocycle is optionally substituted with one or more substituents independentlyAttorney Docket No. 00415-0062-00304 selected from halogen. -OR4, -SR4, -N(R4)2. -N+(R5)3. -C(O)OR4. -P(O)(OR6)2. -P(O)R6(OR6). - S(O)2OR6, -S(O)2R4, and =0. In some instances, R4is independently selected at each occurrence from hydrogen, Ci-io alkyl, and Ci-io heteroalkyl. In some examples, the Ci-io alkyl or Ci-io heteroalkyl is optionally substituted with one or more substituents independently selected from: halogen, -OR8. -SR8. -N(R8)2, -N (R5)3, -C(O)OR8, -P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6. - S(O)2R8, =0, and C3-io carbocycle. In some examples, each C3-io carbocycle is optionally substituted with one or more substituents independently selected from halogen, -OR8, Ci-6 alky l, Ci-6 haloalkyl, Ci-6 hydroxy alkyl, and =0. In some instances, R5is independently selected at each occurrence from hydrogen and Ci-4 alkyl. In some instances, R6is independently selected at each occurrence from hydrogen, Ci-6 alkyl, and -CN. In some instances, R7is selected from C3-io carbocycle and 3- to 10-membered heterocycle, wherein each C3-10 carbocycle and 3- to 10- membered heterocycle is optionally substituted with one or more substituents independently selected from -OH, Ci-6 alkyl, Ci-6 haloalkyl, Ci-6 hy droxy alkyl, and =0. In some instances, R8is selected from hydrogen and Ci-4 alkyl. In some instances, when R1is hydrogen, R2is not hydrogen. In some instances, when R2is hydrogen, R1is not hydrogen.

[0063] In some instances, R1or R2is -N(R4)2, -N(R7), -P(OR6)N(R6)2, or Ci-io alky l. In some instances, R1or R2comprise a mono, di, tri or polyphosphate. In some examples, the polyphosphate is a hexaphosphate. In some instances, the polyphosphate comprises at least three phosphates. In some instances, R4is independently selected at each occurrence from hydrogen and Ci-io alkyl. In some examples, the Ci-io alkyl is substituted with one or more substituents, wherein the one or more substituents is a C3-io carbocycle. In some examples, the C3-10 carbocycle substituted with -OR8. In some instances, R8is a Ci-4 alkyl.

[0064] In some instances, R1or R2has the structureIn some instances, R7is a C3-10 carbocycle. In some examples, the C3-10 carbocycle is substituted with =0. In some example, R1or R2has the structure(e.g., FIG. 5B). In some instances, R6is independently selected at each occurrence from Ci-6 alkyl and -CN. In someAttorney Docket No. 00415-0062-00304 examples, R1or R2has the structure:some instances, theCi-io alkyl is substituted with -OR4. In some examples, R4is a C1-10 alkyl. In some examples, R1MeO-^- or R2has the structure: (e.g., FIG. 5A). In some examples, the composition comprises the structure from a compound of Table 1.Table 1Attorney Docket No. 00415-0062-00304Attorney Docket No. 00415-0062-00304

[0065] Provided herein are methods for polynucleotide synthesis comprising the compositions described herein. In some instances, synthesis comprises phosphoramidite synthesis. In some instances, synthesis comprises enzymatic synthesis. In some instances, synthesis comprises electrochemical synthesis. The electrochemical synthesis may comprise aqueous or organic solvent-based electrochemical synthesis. In some instances, the compositions and respective one or more protecting groups are selected based on the synthesis method.

[0066] Methods for polynucleotide synthesis can generally comprise deprotecting a first protected nucleotide to generate a deprotected nucleotide. The protecting group on the firstAttorney Docket No. 00415-0062-00304 protected nucleotide may comprise any one of the compositions described herein. In some examples, the protecting group is a 5’ protecting group. In some instances, the deprotected nucleotide is contacted with a second protected nucleotide. The second protected nucleotide may also comprise any one of the compositions described herein. In some examples, the second protected nucleotide comprises a 5‘ protecting group. In some examples, the second protected nucleotide comprises a 3’ protecting group, which may be removed prior to contact with the deprotected nucleotide. In some instances, contacting the second protected nucleotide and the deprotected nucleotide comprises coupling the second protected nucleotide to the deprotected nucleotide. Contacting the deprotected nucleotide and the second protected nucleotide can result in extension of the polynucleotide. The one or more operations provided herein may be repeated to synthesize the polynucleotide.

[0067] In electrochemical DNA synthesis, deprotection may generally comprise electrochemical deblocking. Electrochemical deblocking can comprise redox compositions which facilitate electrochemical acid generation. In some instances, a composition comprises one or more redox compounds. In some instances, a composition comprises a first redox compound and a second redox compound. In some instances, the first redox compound is a quinone or substituted derivative thereof. In some instances, the second redox compound is a hydroquinone or substituted derivative thereof. In some instances, the first redox compound and the second redox compound are selected such that a redox potential is less than 2 volts. In some instance, a first redox compound is present in a reduced state. In some instance, a second redox compound is present in an oxidized state.

[0068] The concentration of a redox compound may be varied to achieve a desired redox potential. In some instances, a redox compound is present at 0.1-1M. In some instances, a redox compound is present at 0.1-0.5, 0.1-0.9, 0.3-0.7, 0.4-0.6, 0.4-1, 0.5-1, or 0.6-1M. In some instances, a redox compound is present at about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or about IM. In some instances, a redox compound is present at no more than 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or no more than IM. In some instances, a first redox compound is present at 0. 1- 0.5, 0. 1-0.9, 0.3-0.7, 0.4-0.6, 0.4-1, 0.5-1, or 0.6-1M. In some instances, a first redox compound is present at 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or about IM. In some instances, a second redox compound is present at 0.1-0.5, 0.1-0.9, 0.3-0.7, 0.4-0.6, 0.4-1, 0.5-1, or 0.6-1M. In some instances, a second redox compound is present at 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or about IM.

[0069] The redox compositions described herein may comprise additional components. In some instances, a redox composition comprises a salt. In some instances, the salt is an organic salt. InAttorney Docket No. 00415-0062-00304 some instances, the organic salt is a phase-transfer catalyst. In some instances, the organic salt comprises a tetra alkyl ammonium cation. In some instances, the organic salt comprises an tetrabutylammonium cation. In some instances, the organic salt comprises an tetramethylammonium cation. In some instances, the organic salt comprises an hexafluorophosphate cation. In some instances, the organic salt comprises hexafluorophosphate, tetrafluoroborate, tetraphenylborate, hexafluorophosphate, perchlorate, tetrachloroferrate, hexafluoroarsenate, hexafluoroantimonate, pentafluorohy-droxyantimonate, hexachloroantimonate, tetrakispentafluorophenylborate, tetrakis-(pentafluoromethylphenyl) borate, bi(trifluoromethylsulphonyl)amides or tris(trifluoromethylsulphonyl)methides. In some instances, the concentration of a salt (e.g., organic salt) is 10-50 mM. In some instances, the concentration of a salt (e.g., organic salt) is 10-50 mM, 5-100 mM, 15-75 mM, 25-100 mM, 25- 50 mM, 15-25 mM, or 15-50 mM. In some instances, the concentration of a salt (e.g., organic salt) is about 5. 10. 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, or about 65 mM. In some instances, the concentration of a salt (e.g., organic salt) is no more than 5. 10. 15. 20, 25, 30, 35, 40, 45, 50, 55, 60, or no more than 65 mM.

[0070] In some instances, a water compatible and electrochemically deblocking method is utilized using DMT-aminooxyl protected phosphoramidite as susbrates. DMT aminooxyl moiety may be a useful protecting group in spactioselective phosphoramidite electrochemical deblocking process. In some examples, the process is performed on silicon-based microelectrode arrays. In some instances, such an auxiliary group is removed via mild, aqueous electrochemical deblocking (e.g., e-deblock) solution through an acid-generated anodic process. In some instances, the methods herein allow for synthesis of multiple oligonucleotides simultaneously.

[0071] The redox compositions described herein may comprise at least one solvent. Therefore, in some instances, the deprotecting comprises exposing the first protected nucleotide or the second protected nucleotide to a solvent. In some instances, the solvent is an aqueous solvent. In some instances, the solvent is an organic solvent. In some instances, the solvent comprises hydrocarbons (e.g., hexane, decane, benzene, toluene, xylene, isomers thereof, and the like), ethers (e.g., THF, diethyl ether, methyl t-butyl ether, and the like), esters (e.g., methyl acetate, ethyl acetate, tert-butylacetate, etc.), lactones, ketones (e.g., acetone, methyl ethyl ketone, cyclopentanone, and the like), alcohols (e.g., ethanol, butanol, isopropanol, and the like), amides (e.g., DMF, N-methylpyrrolidinone, or other amides), ureas, carbonates (e.g., diethylcarbonate, or other carbonate), carbamates, aldehydes, amines, cyanates, isocyanates, sulfoxides, sulfones, aromatics, heteroaromatics, thiols, phosphoramides, nitriles (e.g., acetonitrile), alkynes, alkenes, alkanes, halogenated solvents (e.g., tetrachloromethane, dichloromethane, chloroform, or otherAttorney Docket No. 00415-0062-00304 halogenated solvent), silanes, perfluorocarbons (C2-C18 perfluorinated branched or straight alkanes such as perfluorohexane, perfluoroheptane, perfluorodecane, perfluoro aromatics such as perfluorobenzene, or other perfluorocarbon), supercritical fluids, ionic liquids, compressed gases, and the like. In some instances, solvents comprise a nitrile, such as acetonitrile. In some instances, solvents comprise an alcohol, such as methanol or ethanol. In some instances, solvents comprise a halogenated solvent, such as di chloromethane, chloroform, or 1,2-di chloromethane. Any of the solvents described herein may be present as a mixture.

[0072] Compositions described herein may be substantially free from bases. In some instances, the base is a non-nucleophilic base. In some instances, base is an amine base. Non-limited examples of amine bases include 2,6-lutidine, diisopropylethylamine, 1,8- diazabicyclo[5.4.0]undec-7-ene (DBU), l,5-Diazabicyclo(4.3.0)non-5-ene (DBN), 2,6-Di-tert- butylpyridine, pyridine, or other amine base. In some instances the base is a phosphazene base, such as Pl-t-Bu, P2-t-Bu, P3-t-Bu, or P4-t-Bu.

[0073] Redox compositions described herein may result in higher levels of spatial control over deblocking. In some instances, neighboring (e.g., adjacent) loci for polynucleotide synthesis which are not subjected to deblocking voltages are not deblocked. In some instances, adjacent loci are deblocked less than 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.01%, 0.005%, 0.001% or less than 0.0001%.

[0074] As discussed, DMT-protected phosphoramidites (e.g., FIG. 1A) are commonly used in oligonucleotide synthesis. Meanwhile, an organic redox solution system may be designed to achieve site-selective DNA synthesis on microelectrode arrays. Such an e-deblock process may, in some instances, requires harsh conditions (e.g., large amount of electrolyte or high current) and unable to be compatible with synthesis processes such as enzymatic DNA synthesis. Thus, a mild, water-based e-deblock protocol may be utilized. A aminoxyl protected (e.g., FIG. IB) substrate may be applied, followed by successful coupling of next nucleotide. However, in some instances an aminoxyl group may be unstable and may be partially removed in the presence of aqueous e-deblock solution. However, both protecting groups may be used to develop a new e- deblock strategy with DMT-aminoxyl protected (e.g., FIG. 1C) oligonucleotide. An exemplary proposed mechanism of DMT-aminooxyl deblocking pathway is illustrated in FIG. 2. A proton triggering the deblocking process can be generated for example by anodic oxidation of hydroquinone.

[0075] Further provided herein are methods for synthesis using quinone-based protected groups. In some instances, benzoquinone oxime protected nucleotide units may be a useful substrate in DNA synthesis. The oxime protecting group can be removed by reduction process compared toAttorney Docket No. 00415-0062-00304 conventional harsh acidic deblocking condition, thus rendering overall gentle condition in DNA chain elongation and potentially allows for assembling longer DNA products. The reduction process can be handled by addition of reducing reagent. Meanwhile, an aqueous, cathodic reduction process can also be developed to electrochemically deprotect oxime and synthesize DNA via silicon-based microelectrode array.

[0076] In some instances, the nucleotide units comprise a quinone oxime protecting group as illustrated in FIG. 5B. An exemplary proposed quinone oxime protected DNA synthesis process is illustrated in FIG. 6. A reductive deblocking process may break the N-0 bond to release either 3’ or 5’ hydroxyl group, thus allowing assembly of the next nucleotide on the deblocked oligonucleotides. In some instances, phosphoramidite chemical deblocking is performed using dithiothreitol (DTT) (e.g., FIGs. 7A-7B). In some instances, phosphoramidite chemical deblocking is performed using methyl blue (MB) (e.g., FIGs. 9A-9B).

[0077] In some instances, methods and compositions provided herein result in a deprotection efficiency of at least 85%. In some examples, the deprotection efficiency is at least about 85%, 87%, 89%, 90%, 92%, 94%, 95%, 96%, 97% 98%, 99%, 99.9%, 99.95%, or 99.99%. In some examples, the deprotection efficiency is about 85%, 87%, 89%, 90%, 92%, 94%, 95%, 96%, 97% 98%, 99%, 99.9%, 99.95%, or 99.99%. In some examples, the deprotection efficiency is at least about 85% to 90%, 85% to 95%, 87% to 92% 87% to 97%, 90% to 95%, 90% to 99%, 90% to 99.99%, 92% to 95%, 92% to 98%, 92% to 99.9%, 95% to 98%, 95% to 99%, 95% to 99.95%, 95% to 99.99%, 98% to 99%, 98% to 99.95%, 98% to 99.99%, 99% to 99.95%, 99% to 99.99%, or 99.95% to 99.99%.

[0078] Synthesis Devices

[0079] Provided herein are devices for polynucleotide synthesis. Such devices in some instances comprise a solid support comprising a plurality of features (or loci) for polynucleotide synthesis. Such devices may comprise conductive elements or electrodes. Such electrodes may function as anodes or cathodes. Polynucleotides comprise a protecting or blocking group bound to a terminal base during at least one synthesis cycle. Application of a voltage through electrodes during a synthesis step in some instances generates a deprotection reagent (such as an acid or other deprotection reagent) which deblocks polynucleotides (removes the protection group). The length of time the voltage is applied, number of times it applied, and other variables have a significant effect on the extent of deprotection, speed of deprotection, and reduction in unwanted side reactions caused by excess deblocking reagents. The geometry of the device's surface and electrodes also may influence the efficiency of the deblocking step.

[0080] Provided herein are devices for polynucleotide synthesis comprising layers of materials.Attorney Docket No. 00415-0062-00304Such devices may comprise any number of layers of materials comprising conductors, semiconductors, or insulative materials. Traditional devices comprise a base layer, conducting materials (one or more conducting layers configured for use as an electrode; conducting materials may be buried in the base layer or above the base layer), and a porous grow th layer surface. In some instances, conductive layer is in electrical contact with layer. Each of such layers may be individually patterned to generate features for polynucleotide synthesis such as pores, holes, wells, channels, or other shape. Various layers of such devices are in some instances combined to form addressable solid supports. Layers or surfaces of such devices may be in fluid communication with solvents, solutes, or other reagents used during polynucleotide synthesis. Further described herein are devices comprising a plurality of surfaces. In some instances, surfaces comprise features for polynucleotides synthesis in proximity to conducting materials. In some instances, devices described herein comprise 1, 2, 5, 10, 50, 100, or even thousands of surfaces per device. In some instances, a voltage is applied to one or more layers of a device described herein to facilitate polynucleotide synthesis. In some instances, a voltage is applied to one or more layers of a device described herein to facilitate a step in polynucleotide synthesis, such as deblocking. Different layers on different surfaces of different devices are often energized with a voltage at varying times or with varying voltages. For example, a positive voltage is applied to a first layer, and a negative voltage is applied to a second layer of the same or a different device. In some instances, one or more layers on different devices are energized, while others are disconnected from a ground. In some instances, base layers comprise additional circuitry, such as complementary' metal-oxide-semiconductors (CMOS) devices. In some instances, various layers of one or more devices are connected laterally via routing, and / or vertically with vias. In some instances, various layers of one or more devices are connected laterally via routing, and / or vertically with vias to a CMOS layer. In some instances, various layers of one or more devices are connected to a CMOS device via wire bonds, pogo pin contacts, or through Si Vias (TSV).

[0081] A first device provided herein comprises a base layer, and a patterned top layer. In some instances, the top layer comprises a conducting material (conducting layer). In some instances, a polynucleotide synthesis surface is formed on the solvent-exposed surface of the base layer.Such a device provides fluid communication between the polynucleotide synthesis surface and the top layer.

[0082] A second device provided herein comprises a base layer, a buried shield electrode, and a patterned top layer. In some instances, the top layers and comprise a conducting material. In some instances, devices comprise a conducting layer present in the base layer. In some instances,Attorney Docket No. 00415-0062-00304 a polynucleotide synthesis surface is formed by pores in the top layer. Such a device provides fluid communication between the polynucleotide synthesis surface and the top layer. In some instances, the buried shield electrode does not contact the synthesis surface or top layer. In some instances, voltage is passed through the shield electrode to influence the flow of ions in a solvent which contacts the synthesis surface. In some instances a different voltage is applied to the shield electrode compared to the voltage applied to the top layer. In some instances, a voltage applied to the shield electrode is synchronized with an adjacent or proximate conducting layer. In some instances, the time between a voltage applied to the shield electrode and the proximate anode is no more than 0.001 microseconds, 0.1, 0.2. 0.5, 0.8, 1.0, 1.2, 1.5, 1.8, 2, 5, 8, 10, 12, 15, 20, 50, 80, or no more than 100 microseconds. In some instances, the time between a voltage applied to the shield electrode and the proximate anode is no more than 0.001 seconds, 0.1, 0.2, 0.5, 0.8, 1.0, 1.2, 1.5, 1.8, 2, 5, 8, 10, 12, 15, 20, 50, 80, or no more than 100 seconds. In some instances, the time between a voltage applied to the shield electrode and the proximate anode is no more than 0.1 microsecond, 0.2, 0.5, 0.8. 1.0, 1.2, 1.5, 1.8. 2, 5, 8. 10. 12, 15, 20, 50, 80, or no more than 100 microseconds. In some instances, the time between a voltage applied to the shield electrode and the proximate anode is about 0.1 microsecond, 0.2, 0.5, 0.8, 1.0, 1.2, 1.5, 1.8, 2, 5, 8, 10, 12, 15, 20, 50, 80, or about 100 microseconds. In some instances, the time between a voltage applied to the shield electrode and the proximate anode is 0.1-1. 0. 1-5, 0. 1-10, 0.1-100, 0.5-10, 0.5-100, 1-10, 1-50, 1-100, 5-50, 10-100 or 50-100 microseconds.

[0083] A third device provided herein comprises a base layer, and an intermediate layer, and a top layer. In some instances, the intermediate layer and layer comprise a conducting material. In some instances, the top layer comprises a polynucleotide synthesis surface. Such a device provides fluid communication between the polynucleotide synthesis surface and the intermediate layer. The polynucleotide synthesis surfaces in some instances are patterned as cylinders, substantially rectangular shapes, channels, or other shape. In some instances, polynucleotide synthesis surfaces are randomly distributed. In some instances, the intermediate layer comprises a thermal oxide. Devices in some instances comprise one or more additional bonding layers between the synthesis surface and the bottom layer.

[0084] A fourth device provided herein comprises a base layer, a first intermediate layer, a top layer. In some instances, the first intermediate comprises a polynucleotide synthesis surface. In some instances, the smallest feature dimension is. In some instances, the smallest feature dimension is proportional to the diffusion distance of a reagent generated proximate to a conducting layer.

[0085] A fifth device provided herein comprises a base layer, a first intermediate layer, a secondAttorney Docket No. 00415-0062-00304 intermediate layer, a top layer. In some instances, polynucleotides are synthesized on top layer. The polynucleotide synthesis surfaces in some instances are patterned as cylinders, substantially rectangular shapes, channels, or other shape. In some instances, polynucleotide synthesis surfaces are randomly patterned. In some instances, the smallest feature dimension is. In some instances, a device comprises additional bonding layers. In some instances, the smallest feature dimension is proportional to the diffusion distance of a reagent generated proximate to a conducting layer. In some instances, a device comprises a conductive layer configured for use as a cathode which is above the plane of one or more conductive layers configured for use as an anode (attached to a lower conductive layer). In some instances, the anode is in fluid communication with one or more loci for polynucleotide synthesis. In another configuration, a conductive layer configured for use as a cathode and located in the same plane as one or more conductive layers configured for use as an anode (attached to a lower conductive layer).

[0086] A sixth device provided herein comprises a plurality of addressable solid supports, which are in fluid communication with the flow cell area. In some instances, such a device is used to evaluate operational variables of the device. Each surface comprises a plurality of features for polynucleotide synthesis surrounded by a conducting layer. In some instances, a device comprises at least 1, 2, 5, 10, 20, 50. or more than 50 addressable solid supports. In some instances, the surfaces comprise a series of patterned features such as pores or wells for polynucleotide synthesis. In some instances, the distances (e.g., pitch distance) between the features for synthesis is about 0.1 um, 0.2 um, 0.5 um, 0.8 um, 1 um, 2 um, 3 um, or 5 um. In some examples, features for synthesis may be referred to as active areas. The smallest feature dimension in some instances is the diameter of the wells and / or the distance between wells. In some instances, a device comprises at least 1. 2. 5, 10, 20, 50. or more than 50 addressable solid supports. In some instances, the surfaces comprise a series of patterned features such as channels for polynucleotide synthesis. The smallest feature dimension in some instances is the width of the channels and / or the distance between channels. The smallest feature dimension in some instances is the width of the channels and / or the distance between channels. In some instances, surfaces are located on a device such to maximize the available surface area. In some instances, the distance between any two surfaces is 5-1000 microns, 10-500, 50-500, 5-100, 3-10, 3-50, 25- 500 or 50-1000 microns. Additional patterns of features are also in some instances used with the devices described herein. In some instances, the pattern of features on a device are random.

[0087] A seventh device described herein comprises a plurality of device arrays (or addressable solid supports), as shown in FIGS. 14A-14E. FIG. 14A shows two such device arrays for clarity, although such devices may comprise any number of device arrays. Nine such deviceAttorney Docket No. 00415-0062-00304 arrays are shown in FIG. 14B. along with routing connections which allow addressable control of individual or groups of device arrays. The system in FIG. 14B comprises three rows (top, middle, bottom) and three columns (left, center, right). Device array 1 is shown at the top left, middle center, and bottom right. Device array 2 is shown at the top center, middle left, middle right, and bottom center. Device array 3 is shown at the top right and bottom left. The routing connections for each row are shown in the order of device array 1 routing, device array 2 routing, and device array 3, routing. In some instances, device array 1 is individually addressable from device arrays 2 and 3. Four such device arrays are shown in FIG. 14C for clarity only; any number of devices may be arrayed in this way. The four devices are addressable in groups 1. 2, and 4 as shown for clarity only; the number of addressable groups in some instances is equal to or less than the number of total device arrays. Conductive layers 902 in some instances generate reagents (e.g., acid) for electrochemical deprotection of biomolecules, such as polynucleotides. In some instances, 902 is configured for use as an anode. In some instances, a conducting layer is also configured for use as a cathode as shown in FIG. 14C. A cross section of devices of FIG. 14C or FIG. 14E are shown in FIG. 14D. In some instances, polynucleotides are synthesized on oxide layer 905. In some instances, polynucleotides are synthesized on conductive layer 902. Such devices are in some instances addressable by a first layer of routing 901a and a second layer of routing 901b. Such devices may comprise any number of routing layers, for example 1, 2, 3, 4, 5, 10, 20, 50, 100, or more than 100 layers of routing. Routing in different horizontal planes in some instances is connected by one or more vertical interconnect accesses (VIAs), 903 and 904. Such devices may comprise any number of vias, for example 1, 2, 3, 4, 5, 10, 20, 50, 100, 1000, or more than 1000 vias per square micron. The number and size of routing and vias in some instances are proportional to the number of addressable solid supports on a device. A device comprising 16 device arrays (similar to FIG. 14C) is shown in FIG. 14E. Routing 901b is superficial to routing 901a in the device. The sixteen device arrays of FIG. 14E are in some instances addressable as seven groups, but other configurations are also consistent with the devices and methods described herein.

[0088] Devices may comprise any number of device arrays. In some instances, devices comprise at least 10, 50, 100, 1000, 10,000, 100,000, or more than 100,000 device arrays in a single device. In some instances, devices comprise about 10. 50, 100, 1000, 10,000, 100,000, or about 100,000 device arrays in a single device. In some instances, devices comprise 10-50, 10-5000, 10-10,000, 100-1000, 100-10,000, 100-100,000, 1000-10,000, or 1000-100,000 device arrays in a single device.

[0089] Device arrays may be scaled to any size or dimensions. In some instances, device arraysAttorney Docket No. 00415-0062-00304 are about 0.01. 0.02. 0.05, 0. 1. 0.2, 0.5, 0.8, 1. 2, 5, 8. or about 10 microns in width. In some instances, device arrays are no more than 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 0.8, 1, 2, 5, 8, or no more than 10 microns in width. In some instances, device arrays are 0.01-10, 0.1-10, 0.1-1, 0.5-1, 1- 10, or 5-30 microns in width. In some instances, device arrays are separated by about 0.01. 0.02, 0.05, 0.1. 0.2, 0.5, 0.8, 1, 2, 5, 8. or about 10 microns. In some instances, device arrays are separated by no more than 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 0.8, 1, 2, 5, 8, or no more than 10 microns. In some instances, device arrays are separated by 0.01-10, 0.1-10, 0.1-1, 0.5-1, 1-10, or 5-30 microns.

[0090] Devices with addressable device arrays may be addressed in different patterns or configurations. In some instances, only specific groups of device arrays are activated simultaneously. In some instances, device arrays are addressed according to. Any number of device arrays may be activated simultaneously. In some instances, about 1%, 2%, 5%, 10%, 20%, 50%, 75%, or about 100% of the device arrays in a device described herein are activated simultaneously. In some instances, no more than 1%, 2%. 5%, 10%, 20%, 50%, 75%, or no more than 99% of the device arrays in a device described herein are activated simultaneously. In some instances, at least 1%, 2%, 5%, 10%, 20%, 50%, 75%, or at least 99% of the device arrays in a device described herein are activated simultaneously.

[0091] Devices described herein may be fabricated using numerous methods, such as masking methods. In some instances, a lift-off fabrication method is used. Lift-off methods in some instances comprises addition of a sacrificial layer (e.g., photoresist or “PR”) to a base layer coated with an oxide layer, addition of a conductive layer, and removal of the sacrificial layer. In some instances, a dry-etch fabrication method is used. Dry-etch methods in some instances comprises addition of one or more layers to a base layer, such as an oxide layer, a first intermediate layer (e g., TiN, or other material), a conductive layer (e.g., platinum), a second intermediate layer (e.g., TiN, or other material), and a sacrificial layer (e.g., photoresist); partial removal of the second intermediate layer to expose the conductive layer; partial removal of the conductive layer to expose the first intermediate layer; partial removal of the first conductive layer to expose the first intermediate layer; and partial removal of the first intermediate layer to expose the oxide layer.

[0092] Electrochemistry

[0093] Provided herein are methods of applying voltage to devices with the redox compositions described herein. Such voltages may result in any number of different effects, such as electrochemical reaction with solvents or solutes. In some instances, apply a voltage results in deblocking or removal of protecting groups on molecules attached to a synthesis surface. InAttorney Docket No. 00415-0062-00304 some instances molecules are polysaccharides, polynucleotides, polypeptides, or other polymer. In some instances, apply a voltage results in deblocking nucleic acids using the devices described herein. Further provided herein are methods wherein the devices described herein are energized with an electrical voltage. In some instances, the electrical voltage is used to deblock oligonucleotides bound to a solid support or surface. Such deblocking in some instances occurs through direct electrochemical reaction of a blocking group on a polynucleotide, or through the generation of deblocking reagents, such as an acid.

[0094] Methods described herein may comprising energizing a device with a voltage (applying a voltage) for a period of time. Applied voltages in some instances form a circuit between a cathode and an anode, leading to current flow through the device, solvent, and / or other components. In some instances, a layer of a device is configured as an anode or cathode. In some instances, a device comprises an anode which is located above the plane of a cathode (“sandwiched’'). In some instances, conductive layer is in electrical contact with layer. In some instances, a device comprises an anode which is located in substantially the same plane of the cathode. Application of voltage in some instances is configured to perform a step of polynucleotide synthesis. In some instances, methods comprise application of a voltage to deblock polynucleotides. In some instances application of a voltage generates a deblocking reagent. In some instances, devices comprise conducting layers in fluid communication with a solvent, wherein the solvent comprises reagents which generate a deblocking reagent. In some instances, the deblocking reagent is an acid. In some instances, the acid is H+.

[0095] Methods described herein may comprise applying a voltage to one or more devices described herein. In some instances, such voltages result in deprotection of molecules (polynucleotides, polypeptides, polysaccharides, or other polymer) at one or more devices or regions. In some instances, application of a voltage at one or more devices results in deprotection of polynucleotides at one or more devices or regions within one or more devices. In some instances, a device is described as “inactive'’ if a deprotection reagent (e.g., acid or other reagent) is not generated at or in the vicinity of a device or region of a device. In some instances, a device is described as “active” if a deprotection reagent (e.g., acid or other reagent) is generated at or in the vicinity of a device or region of a device. In some instances, deprotection of polynucleotides occurs at or near one or more active devices, or regions of one or more active devices. In some instances, both active and inactive devices are energized with voltages. In some instances, voltage is applied to inactive devices in levels which are insufficient to generate a deprotection reagent. In some instances, deprotection comprises application of one or more voltages (or voltage levels) for periods of time. In some instances, a single voltage level is usedAttorney Docket No. 00415-0062-00304 for deprotection of polynucleotides. In some instances, more than one voltage level is used during deprotection. In some instances, a cathode voltage is kept constant at 0V, while the anode voltage is increased from 0V to 2V during a “pulse”. In some instances, a cathode voltage is kept constant at a negative voltage (e.g., -IV or other negative voltage), while the anode voltage is increased from 0V to 2V during a “pulse”. In some instances, a cathode voltage is decreased from 0V to a negative voltage (such as -IV), and an anode voltage is increased from 0V to IV during a “pulse”. In some instances such voltages are synchronized, wherein the decrease in voltage at the cathode and increase in voltage at the anode occur at approximately the same time. In some instances such voltages are synchronized, wherein the decrease in voltage at the cathode and increase in voltage at the anode occur within 1 sec, 0.5 sec, 0. 1 sec, 0.05 sec, 0.01 sec, 0.005 sec, 0.001 sec, or occur within 0.0005 sec of each other. In some instances, two voltage levels are used during a deprotection step. In some instances, two voltage levels are used during a deprotection step, e.g., a positive and neutral voltage. In some instances, two voltage levels are used during a deprotection step, e.g., a positive and negative voltage. In some instances, three voltage levels are used during a deprotection step, e.g., a positive, neutral (or zero / about zero), and negative voltage. Voltage in some instances is applied to multiple electrodes in fluid communication with the same surface, for example between a deblocking electrode and a shield electrode. Voltages between the deblocking electrode and shield electrode are in some instances are synchronized. In some instances, when the difference between the cathode and anode voltages exceeds a threshold, acid or other reagent is generated. In some instances, synchronizing positive anode and negative cathode voltages results in the advantage of reducing the magnitude of the voltages that are necessary to drive a device.

[0096] Devices may be descnbed as circuits between an anode and a cathode. In some instances, such circuits are described as being in device states, such as “on”, “off’, or “alternate resistance”. In some instances, alternate resistance is a high resistance state, or “disconnect” state. In some instances, a high resistance state is a resistance state that is higher than an off state (e.g., low / no voltage in off state, but still connected to a ground). In some instances, a high resistance state provides an effective amount of resistance to reduce current flow through one or more inactive devices. Without being bound by theory, the disconnect state in some instances reduces undesired deprotection at areas adjacent to an on device. In some instances, a high resistance state provides an effective amount of resistance to reduce current flow to near zero in one or more inactive devices. In some instances an off state is generated by zero (or near zero) voltage between an inactive device and a common cathode. In some instances an off state exists even with a minimum voltage applied between an inactive device and a common cathode,Attorney Docket No. 00415-0062-00304 wherein the minimum voltage is below that amount needed for deprotection. In some instances a high resistance state is generated by zero voltage between an inactive device and the cathode and a higher resistance between the inactive devices and a common cathode. In some instances, an off state indicates zero voltage or negative voltage between the anode and active device (cathode). In some instances, an on state indicates positive voltage between the anode and active device (cathode) which is sufficient for deprotection. In some instances, an inactive device is in the off or alternate resistance state. In some instances, an active device (where deprotection is desired) is cycled (pulsed) between one or more on and off states for a period of time. In some instances, an active device (where deprotection is desired) is cycled between one or more on and off states for a period of time and neighboring inactive devices are maintained in an alternative resistance state.

[0097] A voltage may be applied to the cathode in addition to the anode. In some instances, the cathode is biased with a negative voltage relative to ground. In some instances, biasing the voltage (bias voltage) of the cathode reduces the maximum anode voltage needed for electrochemical deprotection (e g., the voltage difference between the anode and cathode will equal the anode voltage plus the magnitude of the negative bias voltage at the cathode). In some instances, a device comprises a contact bias on the cathode. In some instances, a bias voltage at the cathode is switched whenever the anode voltage is switched (e.g.. synched). In some instances, a cathode controls electrochemistry for a single device. In some instances, a cathode controls electrochemistry for a plurality of devices (“common” cathode). In some instances, use of a common cathode results few er transistors needed per device. In some instances, the bias voltage is no more than -0.1. -0.2, -0.3, -0.5. -0.7, -0.9, -1.0 -1.1, -1.2, -1.5, -1.8, -2.0, -2.1, -2.2, or no more than -2.5 volts. In some instances, the biased voltage is at least -0. 1, -0.2. -0.3, -0.5, - 0.7, -0.9, -1.0 -1.1, -1.2, -1.5, -1.8, -2.0, -2.1, -2.2, or at least -2.5 volts. In some instances, the biased voltage is about -0.1, -0.2, -0.3, -0.5, -0.7, -0.9, -1.0 -1.1, -1.2, -1.5, -1.8, -2.0, -2.1, -2.2, or about -2.5 volts. In some instances, the biased voltage is -0.1 to -2.5 volts, -0.2 to -2.5 volts. - 0.5 to -2.5 volts, -1.0 to -2.5 volts. -1.5 to -2.5 volts, -1.0 to -2.0 volts, -0.5 to -1.0 volts, -0.2 to - 1.5 volts, or -2.0 to -2.5 volts.

[0098] The voltage between two layers of a device or surface may be varied. In some instances, a voltage is between the anode and cathode. In some instances the voltage is 0.5-3, 1-3, 1.5-2.5, 1-2.5, or 1.5-2 volts. In some instances, the voltage is at least 0.5. 0.75, 1, 1.2, 1.5, 1.7. 1.9, 2, 2.2, 2.4, or more than 2.4 volts. In some instances, the voltage is about 0.5, 0.75, 1, 1.2, 1.5, 1.7, 1.9, 2, 2.2, 2.4, or about 2.4 volts. In some instances, the voltage is -0.1 to -2.5 volts, -0.2 to -2.5 volts, -0.5 to -2.5 volts, -1.0 to -2.5 volts, -1.5 to -2.5 volts, -1.0 to -2.0 volts, -0.5 to -1.0 volts, -Attorney Docket No. 00415-0062-003040.2 to -1.5 volts, or -2.0 to -2.5 volts. In some instances, a conducting layer of a device is charged with a positive voltage. In some instances, a conducting layer of a device is charged with a negative voltage. In some instances, a first layer of a device is charged with a positive voltage, and a second layer is charged with a negative voltage at the same time.

[0099] The (total) amount of time a voltage is applied may be varied for each synthesis cycle (e g., deblocking, coupling, etc ). Voltage is applied in some instances for no more than 0.1, 0.2, 0.5, 0.8, 1, 2, 5, or no more than 10 seconds. Voltage is applied in some instances for 0.1-10, 0.5-10, 0.5-5, 0.1-5, 2-5, 2-10, 3-10, or 0.1-2 seconds. Voltage is applied in some instances about 0.1, 0.2, 0.5, 0.8, 1, 2, 5. or about 10 seconds. Voltage is applied in some instances for no more than 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500, 800, or no more than 1000 milliseconds (ms). Voltage is applied in some instances for about 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500, 800, or about 1000 milliseconds. Voltage is applied in some instances for 0.1-1000, 0.5-500, 0.5-50, 0.1-5. 2-50, 2-100, 3-200, 0.1-10, 1-100. 1-50. or 0.1-2 milliseconds.

[0100] Voltage may be applied as a single “on’7”off” cycle, or applied as a series of alternating “on” and “off’ cycles to an active device. In some instances an “on” state is a positive voltage or a negative voltage. The application of voltage in the “on” state followed by an “off’ state is in some instances defined as a “pulse.” In some instances, voltage is applied in a series of pulses, such as no more than 1, 2, 3. 4, 5, 6, 7, 8, 10, 20, 50, 80, 100, 110, 120. 150, 180. 200, 220, 250, 300, 500, or more than 500 pulses. In some instances, voltage is applied in a series of pulses, such as at least 1, 2, 3, 4, 5, 6, 7, 8, 10, 20, 50, 80, 100, 110, 120, 150, 180, 200, 220, 250, 300, 500, or at least 500 pulses. In some instances, voltage is applied in a series of pulses, such as 1- 1000, 1-500, 1-300, 10-500, 10-100. 50-500, 50-200, 100-1000, 2-10, 2-8, 20-200, or 300-750 pulses. In some instances, voltage is applied in a series of pulses, such as about 1, 2, 3. 4, 5, 6. 7. 8, 10, 20, 50, 80, 100, 110, 120, 150, 180, 200, 220, 250, 300, 500, or about 500 pulses. In some instances, voltage is applied in a series of pulses, such as no more than 100, 200, 500, 800, 1000, 2000, 5000, 8000, 10000, 11000, 12000, 15000. 18000, 20000, 50000, 80000, 100,000, 200,000, 500,000, 800,000, or more than 1,000.000 pulses. In some instances, voltage is applied in a series of pulses, such as at least 100, 200, 500, 800, 1000, 2000, 5000, 8000, 10000, 11000, 12000, 15000, 18000, 20000, 50000, 80000, 100,000, 200,000, 500,000, 800,000, or at least 1,000,000 pulses. In some instances, voltage is applied in a series of pulses, such as about 100. 200, 500. 800, 1000, 2000, 5000, 8000, 10000, 11000, 12000, 15000. 18000, 20000, 50000, 80000, 100,000, 200,000, 500,000, 800,000, or about 1,000,000 pulses. In some instances, voltage is applied in a series of pulses, such as at least 10-1000, 10-5000, 100-10,000, 1000- 50,000, 10000-100,000, 50000-500,000, 50000-1,000,000, 10,000-100,000 or 500,000-Attorney Docket No. 00415-0062-00304 1,000,000 pulses.

[0101] The voltage application time may be divided by the number of pulses to define a pulse time (or pulse width, or time per pulse). In some instances a pulse time is no more than 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500, 800, or no more than 1000 milliseconds. In some instances, a pulse time is 0 seconds. In some instances, a pulse time is greater than 0 seconds. In some instances a pulse time is no more than 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500, 800, 1000, 2000, or no more than 5000 seconds. In some instances a pulse time is about 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500, 800, or about 1000 milliseconds. In some instances a pulse time is about 0. 1, 0.2, 0.5. 0.8. 1, 2, 5, 10. 20. 50. 100, 200, 500, 800, 1000, 2000, or no more than 5000 seconds. The pulse time in some instances is 0. 1-1000, 0.5-500, 0.5-50, 0. 1-5, 2- 50, 2-100, 3-200, 0.1-10, 1-100, 1-50, or 0.1-2 milliseconds. The pulse time in some instances is 0.1-5000, 0.5-5000, 0.5-2000, 0.1-1000, 2-500, 2-100, 3-200, 0.1-10, 1-1000, 1-500, or 0.1-200 seconds. In some instances a pulse time is no more than 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500. 800, or no more than 1000 microseconds. In some instances a pulse time is about 0. 1, 0.2, 0.5, 0.8. 1 , 2, 5, 10, 20, 50, 100, 200, 500, 800, or about 1000 microseconds. The pulse time in some instances is 0.1-1000, 0.5-500, 0.5-50, 0.1-5, 2-50, 2-100, 3-200, 0.1-10, 1-100, 1-50, or 0.1-2 microseconds. In some instances, a polynucleotide synthesis surface is washed with a solvent in between pulses. In some instances, a polynucleotide synthesis surface is not washed with a solvent in between pulses. In some instances a series of pulses are used to deliver voltage to a surface, followed by a wash step, followed by another series of pulses. Pulses need not be the same voltage. In some instances, a first pulse is positive, and a second pulse is negative. In some instances, the time between a positive and negative voltage is substantially instantaneous. In some instances, a first pulse is about 2 volts and a second pulse is about -0.6 volts. In some instances, a first pulse is 0.5 to 3 volts and a second pulse is -0. 1 to -1.0 volts.

[0102] The time period between pulses may be varied to allow, without being bound by theory', electrochemically generated reagents to dissipate. The time between pulses in some instances is no more than 0. 1, 0.2, 0.5, 0.8. 1, 2, 5. or no more than 10 seconds. The time between pulses in some instances is 0.1-10, 0.5-10, 0.5-5, 0.1-5, 2-5, 2-10, 3-10, or 0.1-2 seconds. The time between pulses in some instances is about 0.1, 0.2, 0.5, 0.8, 1, 2, 5, or about 10 seconds. The time between pulses in some instances is no more than 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500. 800, or no more than 1000 milliseconds (ms). The time between pulses in some instances is about 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500, 800, or about 1000 milliseconds. The time between pulses in some instances is 0.1-1000, 0.5-500, 0.5-50, 0.1-5, 2- 50, 2-100, 3-200, 0.1-10, 1-100, 1-50, or 0.1-2 milliseconds. The time between pulses in someAttorney Docket No.00415-0062-00304 instances is no more than 0.1, 0.2.0.5.0.8. 1, 2.5, 10.20.50. 100, 200.500, 800, or no more than 1000 microseconds (ms). The time between pulses in some instances is about 0.1, 0.2, 0.5, 0.8. 1, 2, 5, 10, 20, 50, 100, 200, 500, 800, or about 1000 microseconds. The time between pulses in some instances is 0.1-1000, 0.5-500, 0.5-50, 0.1-5, 2-50, 2-100, 3-200, 0.1-10, 1-100, 1-50. or 0.1-2 microseconds. In some instances, the ratio between on and off times for series of pulses is described as a duty cycle. In some instances, aduty cycle is about 1:100, 1:50, 1:20, 1:10, 1:5, 1:2, 1:1.5, 1:1.05, 1.05:1, 1.5: 1, 2:1, or about 3:1. In some instances, a duty cycle is no more than 1:100, 1:50, 1:20, 1:10, 1:5, 1:2, 1:1.5, 1:1.05, 1.05:1, 1.5:1, 2:1, or no more than 3 : 1. In some instances, a duty cycle is at least 1:100.1:50, 1:20, 1:10, 1:5, 1:2, 1:1.5, 1:1.05, 1.05:1, 1.5:1, 2:1, oratleast3:l.

[0103] Various chemical reactions may be used to deblock polynucleotides, directly or indirectly. In some instances electrical voltage oxidizes or reduces a blocking group (protecting group) directly on a polynucleotide, causing the polynucleotide to be deblocked. In some instances, the voltage generates an in-situ reagent which deblocks the blocked nucleotide. In some instances, the polynucleotide comprises an acid-cleavable blocking group. In some instances, the reagent is dissolved in a solvent. In some instances, the reagent is an acid, such as H+. Various reagents may be used to electrochemically generate deblocking reagents such as acids. In some instances, a reagent comprises a quinone. In some instances, the quinone is benzoquinone, hydroquinone, anthraquinone, substituted benzoquinone, a hydrazine, a diazirine, or other reagent configured to generate an acid when a voltage is applied. In some instances, the reagent comprises a mixture of hy droquinone (HQ) and benzoquinone (BQ). In some instances, the reagent comprises a mixture of hydroquinone and benzoquinone, wherein the ratio of HQ:BQ is about 100:1, 50:1.20:1. 10:1.8:1, 5:1, 3:1.2:1, 1:1, 1:2. 1:5. or about 1:10. In some instances, the ratio of HQ:BQ is at least 100:1, 50:1, 20:1, 10:1, 8:1, 5:1, 3:1, 2:1, or at least 1:1. In some instances, the ratio ofHQ:BQ is no more than 100:1, 50:1, 20:1, 10:1, 8:1, 5:1, 3:1, 2:1, or no more than 1:1. In some instances, the ratio of HQ:BQ is 100: 1-10:1, 50:1-1:1, 20:1-5:1, 15:1-5:1. 10:1-1:1. 10:1-2:1.20:1-2:1. 1:1-1:5, 1:1-10:110:1-1:10, or 5:1-1:5.

[0104] Provided herein are methods of fabricating the devices and surfaces for polynucleotide synthesis. Described herein are layers integrated into a solid support. In some instances, layers comprise electrodes or are configured for use as electrodes. In some instances, electrodes are configured as cathodes or anodes. In some instances, an anode comprises a metal oxide. In some instances, nucleic acids are synthesized on an anode. In some instances, nucleic acids are synthesized on a metal oxide layer. In some instances, nucleic acids are synthesized on a porous metal oxide layer comprising a continuous metal layer beneath it. Electrodes in some instancesAttorney Docket No. 00415-0062-00304 comprise at least one conductor, and are fabricated of materials well known in the art. In some instances, electrodes comprise at least one conductor and one or more insulators or semiconductors. Materials may comprise metals, non-metals, mixed-metal oxides, nitrides, carbides, silicon-based materials, or other material. In some instances, metal oxides include TiO2, Ta2O5. IrO2. RuO2, RhO2, Nb2O5. A12O3. BaO. Y2O3, HfO2, SrO or other metal oxide known in the art. In some instances, metal carbides include TiC, WC, ThC2, ThC, VC, W2C, ZrC, HfC, NbC, TaC, Ta2C, or other metal carbide known in the art. In some instances, metal nitrides include GaN, InN, BN, Be3N2, Cr2N, MoN, Si3N4, TaN. Th2N2, VN, ZrN, TiN, HfN, NbC, WN, TaN, or other metal nitride known in the art. In some instances, a device disclosed herein is manufactured with a combination of materials listed herein or any other suitable material known in the art.

[0105] Solid supports comprising layers may be coated with additional materials such as semiconductors or insulators. In some instances, a layer is configured for use as an electrode. In some instances, electrodes are coated with materials for polynucleotide attachment and synthesis. Each electrode can control one, or a plurality of different loci for synthesis, wherein each locus for synthesis has a density of polynucleotides. In some instances, the density is at least 1 oligo per 10 nm2, 20, 50, 100, 200. 500, 1,000, 2,000, 5,000 or at least 1 oligo per 10,000 nm2. In some instances, the density is about 1 oligo per 10 nm2 to about 1 oligo per 5,000 nm2, about 1 oligo per 50 nm2 to about 1 oligo per 500 nm2, or about 1 oligo per 25 nm2 to about 1 oligo per 75 nm2. In some instances, the density of polynucleotides is about 1 oligo per 25 nm2 to about 1 oligo per 75 nm2.

[0106] Described herein are devices wherein two or more solid supports are assembled. In some instances, solid supports are interfaced together on a larger unit. Interfacing may compnse exchange of fluids, electrical signals, or other medium of exchange between solid supports. This unit is capable of interface with any number of servers, computers, or networked devices. For example, a plurality of solid support is integrated onto a rack unit, which is conveniently inserted or removed from a server rack. The rack unit may comprise any number of solid supports. In some instances the rack unit comprises at least 1, 2, 5, 10, 20, 50, 100, 200, 500, 1000, 2000, 5000, 10,000, 20,000, 50,000, 100,000 or more than 100,000 solid supports. In some instances, two or more solid supports are not interfaced with each other. Nucleic acids (and the information stored in them) present on solid supports can be accessed from the rack unit. In some instances, solid supports are present on solid supports such as chips. Access includes removal of polynucleotides from solid supports, direct analysis of polynucleotides on the solid support, or any other method which allows the information stored in the nucleic acids to be manipulated orAttorney Docket No. 00415-0062-00304 identified. Information in some instances is accessed from a plurality of racks, a single rack, a single solid support in a rack, a portion of the solid support, or a single locus on a solid support. In various instances, access comprises interfacing nucleic acids with additional devices such as mass spectrometers, HPLC, sequencing instruments, PCR thermocyclers, or other device for manipulating nucleic acids. Access to nucleic acid information in some instances is achieved by cleavage of polynucleotides from all or a portion of a solid support. Cleavage in some instances comprises exposure to chemical reagents (ammonia or other reagent), electrical potential, radiation, heat, light, acoustics, or other form of energy capable of manipulating chemical bonds. In some instances, cleavage occurs by charging one or more electrodes in the vicinity of the polynucleotides. In some instances, electromagnetic radiation in the form of UV light is used for cleavage of polynucleotides. In some instances, a lamp is used for cleavage of polynucleotides, and a mask mediates exposure locations of the UV light to the surface. In some instances, a laser is used for cleavage of polynucleotides, and a shutter opened / closed state controls exposure of the UV light to the surface. In some instances, access to nucleic acid information (including removal / addition of racks, solid supports, reagents, nucleic acids, or other component) is completely automated.

[0107] Solid supports as described herein comprise an active area. In some instances, the active area comprises addressable solid supports, regions, or loci for nucleic acid synthesis. In some instances, the active area comprises addressable regions or loci for nucleic acid storage. In some instances, an active area is in fluid communication with solvents or other reagents. The active area comprises vary ing dimensions. For example, the dimension of the active area is between about 1 mm to about 50 mm by about 1 mm to about 50 mm. In some instances, the active area comprises a width of at least or about 0.5. 1. 1.5, 2, 2.5. 3, 5, 5. 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, or more than 80 mm. In some instances, the active area comprises a height of at least or about 0.5, 1, 1.5, 2, 2.5, 3, 5, 5, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, or more than 80 mm. An exemplary active area within a solid support is seen in FIG. 5C. A package 4207 comprises an active area 4205 within a solid support 4203. The package 4207 also comprises a fluidics interface 4201.

[0108] Described herein are devices, compositions, systems and methods for solid support based nucleic acid synthesis and storage, wherein the solid support has a number of sites (e.g., spots) or positions for synthesis or storage. In some instances, the solid support comprises up to or about 10,000 by 10,000 positions in an area. In some instances, the solid support comprises between about 1000 and 20,000 by betw een about 1000 and 20,000 positions in an area. In some instances, the solid support comprises at least or about 10, 30, 50, 75, 100, 200, 300, 400, 500,Attorney Docket No. 00415-0062-003041000, 2000, 3000, 4000. 5000. 6000, 7000, 8000, 9000. 10.000. 12.000, 14,000, 16,000, 18,000. 20,000 positions by least or about 10, 30, 50, 75, 100, 200, 300, 400, 500, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10,000, 12,000, 14,000, 16,000, 18,000, 20,000 positions in an area. In some instances the area is up to 0.25, 0.5, 0.75, 1.0, 1.25, 1.5, or 2.0 inches squared. In some instances, the solid support comprises addressable loci having a pitch of at least or about 0.1, 0.2, 0.25, 0.3, 0.4, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5, 6, 7, 8, 9, 10, or more than 10 um. In some instances, the solid support comprises addressable loci having a pitch of about 5 um. In some instances, the solid support comprises addressable loci having a pitch of about 2 um. In some instances, the solid support comprises addressable loci having a pitch of about 1 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.2 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.2 um to about 10 um, about 0.2 to about 8 um, about 0.5 to about 10 um, about 1 um to about 10 um. about 2 um to about 8 um, about 3 um to about 5 um, about 1 um to about 3 um or about 0.5 um to about 3 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.1 um to about 3 um. In some instances, the solid support comprises addressable loci having a pitch of at least or about 0.01, 0.02, 0.025, 0.03, 0.04, 0.05, 0.1, 0.15, .02, 0.25, 0.30, 0.35, 0.4, 0.45, 0.5, 0.6, 0.7, 0.8. 0.9, 1, or more than 1 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.5 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.2 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.1 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.02 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.02 um to about 1 um, about 0.02 to about 0.8 um, about 0.05 to about 0. 1 um. about 0.1 um to about 1 um. about 0.2 um to about 0.8 um, about 0.3 um to about 0.5 um, about 0. 1 um to about 0.3 um or about 0.05 um to about 0.3 um. In some instances, the solid support comprises addressable loci having a pitch of about 0.01 um to about 0.3 um.

[0109] The solid support for nucleic acid synthesis or storage as described herein comprises a high capacity for storage of data. For example, the capacity of the solid support is at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more than 1000 petabytes. In some instances, the capacity of the solid support is between about 1 to about 10 petabytes or between about 1 to about 100 petabytes. In some instances, the capacity of the solid support is about 100 petabytes. In some instances, the data is stored as addressable arrays of packets as droplets. In some instances, the data is stored as addressable arrays of packets as droplets on a spot. In some instances, the data is stored as addressable arraysAttorney Docket No. 00415-0062-00304 of packets as dry wells. In some instances, the addressable arrays comprise at least or about 1, 2. 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 200, or more than 200 gigabytes of data. In some instances, the addressable arrays comprise at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 200, or more than 200 terabytes of data. In some instances, an item of information is stored in a background of data. For example, an item of information encodes for about 10 to about 100 megabytes of data and is stored in 1 petabyte of background data. In some instances, an item of information encodes for at least or about 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, or more than 500 megabytes of data and is stored in 1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300. 400, 500, or more than 500 petabytes of background data.

[0110] Nucleic Acid Based Information Storage

[0111] Provided herein are devices, compositions, systems and methods for nucleic acid-based information (data) storage. In a first step, a digital sequence encoding an item of information (i.e., digital information in a binary code for processing by a computer) is received. An encryption scheme is applied to convert the digital sequence from a binary code to a nucleic acid sequence. A surface material for nucleic acid extension, a design for loci for nucleic acid extension (aka, arrangement spots), and reagents for nucleic acid synthesis are selected. The surface of a structure is prepared for nucleic acid synthesis. De novo poly nucleotide synthesis is performed. The synthesized polynucleotides are stored and available for subsequent release, in whole or in part. Once released, the polynucleotides, in whole or in part, are sequenced, subject to decryption to convert nucleic sequence back to digital sequence. The digital sequence is then assembled to obtain an alignment encoding for the original item of information.

[0112] Items of Information

[0113] Optionally, an early step of data storage process disclosed herein includes obtaining or receiving one or more items of information in the form of an initial code. Items of information include, without limitation, text, audio and visual information. Exemplary' sources for items of information include, without limitation, books, periodicals, electronic databases, medical records, letters, forms, voice recordings, animal recordings, biological profiles, broadcasts, films, short videos, emails, bookkeeping phone logs, internet activity logs, drawings, paintings, prints, photographs, pixelated graphics, and software code. Exemplary biological profile sources for items of information include, without limitation, gene libraries, genomes, gene expression data, and protein activity data. Exemplary formats for items of information include, without limitation, .txt, .PDF, .doc, .docx, .ppt, .pptx, .xls, .xlsx, .rtf, .jpg, .gif, .psd, .bmp, .tiff, .png, and. mpeg. The amount of individual file sizes encoding for an item of information, or a plurality' of files encoding for items of information, in digital format include, without limitation, up to 1024Attorney Docket No. 00415-0062-00304 bytes (equal to 1 KB), 1024 KB (equal to 1MB), 1024 MB (equal to 1 GB), 1024 GB (equal to 1TB), 1024 TB (equal to 1PB), 1 exabyte, 1 zettabyte, 1 yottabyte, 1 xenottabyte or more. In some instances, an amount of digital information is at least 1 gigabyte (GB). In some instances, the amount of digital information is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 200, 300, 400, 500, 600. 700, 800, 900, 1000 or more than 1000 gigabytes. In some instances, the amount of digital information is at least 1 terabyte (TB). In some instances, the amount of digital information is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more than 1000 terabytes. In some instances, the amount of digital information is at least 1 petabyte (PB). In some instances, the amount of digital information is at least 1. 2, 3, 4. 5, 6, 7, 8, 9, 10, 20, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more than 1000 petabytes. In some instances, items of information are encoded using with an encoding scheme (e.g., 2 bits per base, 3 bits per base, or other encoding scheme).

[0114] Structures for polynucleotide synthesis

[0115] Provided herein are rigid or flexibles structures for polynucleotide synthesis. In the case of rigid structures, provided herein are devices having a structure for the generation of a library of polynucleotides. In some instances, the structure comprises a plate.

[0116] In the case of flexible structures, provided herein are devices wherein the flexible structure comprises a continuous loop wrapped around one or more fixed structures, e.g., a pair of rollers or a non-continuous flexible structure wrapped around separate fixed structures, e.g., a pair reels. In some instances, the structures comprise multiple regions for polynucleotide synthesis. An exemplary structure comprises a plate with distinct regions for polynucleotide synthesis. The distinct regions may be separated by breaking or cutting. Each of the distinct regions may be further released, sequenced, decrypted, and read or stored. An alternative structure comprises a tape comprises with distinct regions for polynucleotide synthesis. The distinct regions may be separated by breaking or cutting. Each of the distinct regions may be further released, sequenced, decrypted, and read or stored. Provided herein are flexible structures having a surface with a plurality of loci for polynucleotide extension. Each locus in a portion of the flexible structure, may be a substantially planar spot (e g., flat), a channel, or a well. In some instances, each locus of the structure has a width of about 10 um and a distance between the center of each structure of about 21 um. In some instances, each locus of the structure has a width of about 1 um and a distance between the center of each structure of about 2 um. In some instances, each locus of the structure has a width of about 0. 1 um and a distance between the center of each structure of about 0.2 um. Loci may comprise, without limitation, circular, rectangular, tapered, or rounded shapes. Alternatively or in combination, the structures are rigid.Attorney Docket No. 00415-0062-00304In some instances, the rigid structures comprise loci for polynucleotide synthesis. In some instances, the rigid structures comprise substantially planar regions, channels, or wells for polynucleotide synthesis.

[0117] In some instances, a well described herein has a width to depth (or height) ratio of 1 to 0.01, wherein the width is a measurement of the width at the narrowest segment of the well. In some instances, a well described herein has a width to depth (or height) ratio of 0.5 to 0.01, wherein the width is a measurement of the width at the narrowest segment of the well. In some instances, a w ell described herein has a width to depth (or height) ratio of about 0.01, 0.05, 0.1, 0.15, 0.16, 0.2. 0.5, or 1. Provided herein are structures for polynucleotide synthesis comprising a plurality of discrete loci for polynucleotide synthesis. Exemplary structures for the loci include, without limitation, substantially planar regions, channels, wells or protrusions. Structures described herein may comprise a plurality of clusters, each cluster comprising a plurality of w ells, loci or channels. Alternatively, described herein may comprise a homogenous arrangement of wells, loci or channels. Structures provided herein may comprise wells having a height or depth from about 5 um to about 500 um, from about 5 um to about 400 um, from about 5 um to about 300 um, from about 5 um to about 200 um, from about 5 um to about 100 um, from about 5 um to about 50 um, or from about 10 um to about 50 um. In some instances, the height of a well is less than 100 um, less than 80 um, less than 60 um, less than 40 um or less than 20 um. In some instances, well height is about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500 um or more. In some instances, the height or depth of the well is at least 10, 25, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more than 1000 nm. In some instances, the height or depth of the well is in a range of about 10 nm to about 1000 nm, about 25 nm to about 900 nm, about 50 nm to about 800 nm, about 75 nm to about 700 nm, about 100 nm to about 600 nm, or about 200 nm to about 500. In some instances, the height or depth of the well is in a range of about 50 nm to about 1 um. In some instances, well height is about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100. 200, 300, 400, 500, 700, 800, 900 or about 1000 nm.

[0118] Structures for polynucleotide synthesis provided herein may comprise channels. The channels may have a width to depth (or height) ratio of 1 to 0.01, wherein the width is a measurement of the width at the narrow est segment of the microchannel. In some instances, a channel described herein has a width to depth (or height) ratio of 0.5 to 0.01, wherein the width is a measurement of the width at the narrowest segment of the microchannel. In some instances, a channel described herein has a width to depth (or height) ratio of about 0.01, 0.05, 0. 1, 0. 15, 0.16, 0.2, 0.5, or l.

[0119] Described herein are structures for polynucleotide synthesis comprising a plurality ofAttorney Docket No. 00415-0062-00304 discrete loci. Structures comprise, without limitation, substantially planar regions, channels, protrusions, or wells for polynucleotide synthesis. In some instances, structures described herein are provided comprising a plurality of channels, wherein the height or depth of the channel is from about 5 um to about 500 um, from about 5 um to about 400 um, from about 5 um to about 300 um, from about 5 um to about 200 um, from about 5 um to about 100 um, from about 5 um to about 50 um, or from about 10 um to about 50 um. In some cases, the height of a channel is less than 100 um, less than 80 um, less than 60 um, less than 40 um or less than 20 um. In some cases, channel height is about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500 um or more. In some instances, the height or depth of the channel is at least 10, 25, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more than 1000 nm. In some instances, the height or depth of the channel is in a range of about 10 nm to about 1000 nm, about 25 nm to about 900 nm, about 50 nm to about 800 nm, about 75 nm to about 700 nm, about 100 nm to about 600 nm, or about 200 nm to about 500. Channels described herein may be arranged on a surface in clusters or as a homogenous field.

[0120] The width of a locus on the surface of a structure for polynucleotide synthesis described herein may be from about 0. 1 um to about 500 um, from about 0.5 um to about 500 um, from about 1 um to about 200 um. from about 1 um to about 100 um, from about 5 um to about 100 um, or from about 0. 1 um to about 100 um, for example, about 90 um, 80 um, 70 um, 60 um, 50 um, 40 um, 30 um, 20 um, 10 um, 5 um, 1 um or 0.5 um. In some instances, the width of a locus is less than about 100 um, 90 um, 80 um, 70 um, 60 um, 50 um, 40 um, 30 um, 20 um or 10 um. In some instances, the width of a locus is at least 10, 25, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800. 900, 1000, or more than 1000 nm. In some instances, the width of a locus is in a range of about 10 nm to about 1000 nm. about 25 nm to about 900 nm, about 50 nm to about 800 nm, about 75 nm to about 700 nm, about 100 nm to about 600 nm, or about 200 nm to about 500. In some instances, the width of a locus is in a range of about 50 nm to about 1000 nm. In some instances, the distance between the center of two adjacent loci is from about 0. 1 um to about 500 um, 0.5 um to about 500 um, from about 1 um to about 200 um, from about 1 um to about 100 um, from about 5 um to about 200 um, from about 5 um to about 100 um, from about 5 um to about 50 um, or from about 5 um to about 30 um, for example, about 20 um. In some instances, the total width of a locus is about 5 um, 10 um, 20 um, 30 um, 40 um, 50 um, 60 um. 70 um, 80 um, 90 um. or 100 um. In some instances, the total width of a locus is about 1 um to 100 um, 30 um to 100 um, or 50 um to 70 um. In some instances, the distance between the center of two adjacent loci is from about 0.5 um to about 2 um, 0.5 um to about 2 um, from about 0.75 um to about 2 um, from about 1 um to about 2 um, from about 0.2 um to about 1 um, from about 0.5Attorney Docket No. 00415-0062-00304 um to about 1.5 um, from about 0.5 um to about 0.8 um, or from about 0.5 um to about 1 um, for example, about 1 um. In some instances, the total width of a locus is about 50 nm, 0. 1 um, 0.2 um, 0.3 um, 0.4 um, 0.5 um, 0.6 um, 0.7 um, 0.8 um, 0.9 um, 1 um, 1.1 um, 1.2 um, 1.3 um, 1.4 um, or 1.5 um. In some instances, the total width of a locus is about 0.5 um to 2 um, 0.75 um to 1 um, or 0.9 um to 2 um.

[0121] In some instances, each locus supports the synthesis of a population of polynucleotides having a different sequence than a population of polynucleotides grow n on another locus. Provided herein are surfaces which comprise at least 10, 100, 256, 500, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000. 10000, 11000, 12000, 13000, 14000, 15000, 20000, 30000. 40000, 50000 or more clusters. Provided herein are surfaces which comprise more than 2,000; 5,000; 10,000; 20,000; 30,000; 50,000; 100,000; 200,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 900,000; 1,000,000; 5,000,000; or 10,000,000 or more distinct loci. In some cases, each cluster includes 1, 2, 3, 4, 5, 6. 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 130, 150. 200, 500 or more loci. In some cases, each cluster includes 50 to 500, 50 to 200, 50 to 150, or 1 0 to 150 loci. In some cases, each cluster includes 100 to 150 loci. In some instances, each cluster includes 109, 121, 130 or 137 loci.

[0122] Provided herein are loci having a width at the longest segment of 5 to 100 um. In some cases, the loci have a width at the longest segment of about 30, 35, 40, 45, 50, 55 or 60 um. In some cases, the loci are channels having multiple segments, wherein each segment has a center to center distance apart of 5 to 50 um. In some cases, the center to center distance apart for each segment is about 5, 10, 15, 20 or 25 um.

[0123] Provided herein are loci having a width at the longest segment of 5 to 500 nm. In some cases, the loci have a width at the longest segment of about 30, 35, 40, 45, 50, 55, 60, 80, or 100 nm. In some cases, the loci are channels having multiple segments, wherein each segment has a center to center distance apart of 5 to 50 nm. In some cases, the center to center distance apart for each segment is about 5, 10, 15, 20, 25, 50, 100, or 200 nm.

[0124] In some instances, the number of distinct polynucleotides synthesized on the surface of a structure described herein is dependent on the number of distinct loci available in the substrate. In some instances, the density of loci within a cluster of a substrate is at least or about 1 locus per mm2, 10 loci per mm2, 25 loci per mm2, 50 loci per mm2, 65 loci per mm2, 75 loci per mm2, 100 loci per mm2. 130 loci per mm2, 150 loci per mm2, 175 loci per mm2, 200 loci per mm2, 300 loci per mm2, 400 loci per mm2, 500 loci per mm2, 1,000 loci per mm2, 104 loci per mm2, 105 loci per mm2, 106 loci per mm2, or more. In some cases, a substrate comprises from about 10 loci per mm2 to about 500 mm2, from about 25 loci per mm2 to about 400 mm2, fromAttorney Docket No. 00415-0062-00304 about 50 loci per mm2 to about 500 mm2, from about 100 loci per mm2 to about 500 mm2, from about 150 loci per mm2 to about 500 mm2, from about 10 loci per mm2 to about 250 mm2, from about 50 loci per mm2 to about 250 mm2, from about 10 loci per mm2 to about 200 mm2, or from about 50 loci per mm2 to about 200 mm2. In some cases, a substrate comprises from about 104 loci per mm2 to about 105 mm2. In some cases, a substrate comprises from about 105 loci per mm2 to about 107 mm2. In some cases, a substrate comprises at least 105 loci per mm2. In some cases, a substrate comprises at least 106 loci per mm2. In some cases, a substrate comprises at least 107 loci per mm2. In some cases, a substrate comprises from about 104 loci per mm2 to about 105 mm2. In some instances, the density of loci within a cluster of a substrate is at least or about 1 locus per um2, 10 loci per um2, 25 loci per um2, 50 loci per um2, 65 loci per um2, 75 loci per um2, 100 loci per um2, 130 loci per um2, 150 loci per um2, 175 loci per um2, 200 loci per um2, 300 loci per um2, 400 loci per um2, 500 loci per um2, 1,000 loci per um2 or more. In some cases, a substrate comprises from about 10 loci per um2 to about 500 um2. from about 25 loci per um2 to about 400 um2. from about 50 loci per um2 to about 500 um2, from about 100 loci per um2 to about 500 um2, from about 150 loci per um2 to about 500 um2, from about 10 loci per um2 to about 250 um2, from about 50 loci per um2 to about 250 um2, from about 10 loci per um2 to about 200 um2, or from about 50 loci per um2 to about 200 um2.

[0125] In some instances, the distance between the centers of two adjacent loci within a cluster is from about 10 um to about 500 um, from about 10 urn to about 200 um, or from about 10 um to about 100 um. In some cases, the distance between two centers of adjacent loci is greater than about 10 um. 20 um, 30 um, 40 um, 50 um, 60 um, 70 um, 80 um, 90 um or 100 um. In some cases, the distance between the centers of two adjacent loci is less than about 200 um, 150 um. 100 um, 80 um, 70 um, 60 um, 50 um, 40 um, 30 um, 20 um or 10 um. In some cases, the distance between the centers of two adjacent loci is less than about 10000 nm, 8000 nm, 6000 nm, 4000 nm, 2000 nm 1000 nm, 800 nm, 600 nm, 400 nm, 200 nm, 150 nm, 100 nm, 80 um, 70 nm, 60 nm. 50 nm. 40 nm. 30 nm. 20 nm or 10 nm. In some instances, each square meter of a structure described herein allows for at least 107, 108, 109, 1010, 1011 loci, where each locus supports one polynucleotide. In some instances, 109 polynucleotides are supported on less than about 6, 5, 4, 3, 2 or 1 m2 of a structure described herein.

[0126] In some instances, a structure described herein provides support for the synthesis of more than 2,000; 5,000; 10,000; 20,000; 30,000; 50,000; 100,000; 200,000; 300,000; 400,000;500,000; 600,000; 700,000; 800,000; 900,000; 1,000,000; 1,200,000; 1,400,000; 1,600,000; 1,800,000; 2,000,000; 2,500,000; 3,000,000; 3,500,000; 4,000,000; 4,500,000; 5,000,000;Attorney Docket No. 00415-0062-0030410.000.000 or more non-identical polynucleotides. In some cases, the structure provides support for the synthesis of more than 2,000; 5,000; 10,000; 20,000; 50,000; 100,000; 200,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 900,000; 1,000,000; 1,200,000; 1,400,000;1,600,000; 1,800,000; 2,000,000; 2,500,000; 3,000,000; 3,500,000; 4,000,000; 4,500,000;5,000,000; 10,000.000 or more polynucleotides encoding for distinct sequences. In some instances, at least a portion of the polynucleotides have an identical sequence or are configured to be synthesized with an identical sequence. In some instances, the structure provides a surface environment for the growth of polynucleotides having at least 50, 60, 70, 75, 80, 85, 90, 95, 100, 110, 120. 130, 140, 150, 160, 175. 200, 225, 250, 275, 300, 325, 350. 375, 400, 425, 450, 475. 500 bases or more. In some arrangements, structures for polynucleotide synthesis described herein comprise sites for polynucleotide synthesis in a uniform arrangement.

[0127] In some instances, polynucleotides are synthesized on distinct loci of a structure, wherein each locus supports the synthesis of a population of polynucleotides. In some cases, each locus supports the synthesis of a population of polynucleotides having a different sequence than a population of polynucleotides grown on another locus. In some instances, the loci of a structure are located within a plurality' of clusters. In some instances, a structure comprises at least 10, 500, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 11000, 12000, 13000, 14000, 15000, 20000, 30000, 40000, 50000 or more clusters. In some instances, a structure comprises more than 2,000; 5,000; 10,000; 100,000; 200,000; 300,000; 400,000; 500,000;600,000; 700,000; 800,000; 900,000; 1,000,000; 1,100,000; 1,200,000; 1,300,000; 1,400,000; 1,500,000; 1,600,000; 1,700,000; 1,800,000; 1,900,000; 2,000,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 900.000; 1,000,000; 1,200,000; 1,400,000; 1,600,000; 1.800,000;2,000,000; 2.500,000; 3.000,000; 3,500.000; 4,000.000; 4,500.000; 5,000,000; or 10,000,000 or more distinct loci. In some cases, each cluster includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 130, 150 or more loci. In some instances, each cluster includes 50 to 500, 100 to 150, or 100 to 200 loci. In some instances, each cluster includes 109, 121, 130 or 137 loci. In some instances, each cluster includes 5. 6, 7, 8, 9. 10. 11 or 12 loci. In some instances, polynucleotides from distinct loci within one cluster have sequences that, when assembled, encode for a contiguous longer polynucleotide of a predetermined sequence.

[0128] Structure size

[0129] In some instances, a structure described herein is about the size of a plate (e.g., chip), for example between about 40 and 120 mm by between about 25 and 100 mm. In some instances, a structure described herein has a diameter less than or equal to about 1000 mm, 500 mm, 450 mm, 400 mm, 300 mm, 250 nm, 200 mm, 150 mm, 100 mm or 50 mm. In some instances, theAttorney Docket No. 00415-0062-00304 diameter of a substrate is between about 25 mm and 1000 mm, between about 25 mm and about 800 mm, between about 25 mm and about 600 mm, between about 25 mm and about 500 mm, between about 25 mm and about 400 mm, between about 25 mm and about 300 mm, or between about 25 mm and about 200. Non-limiting examples of substrate size include about 300 mm, 200 mm, 150 mm, 130 mm, 100 mm, 84 mm, 76 mm, 54 mm, 51 mm and 25 mm. In some instances, a substrate has a planar surface area of at least 100 mm2; 200 mm2; 500 mm2; 1,000 mm2; 2,000 mm2; 4,500 mm2; 5,000 mm2; 10,000 mm2; 12,000 mm2; 15,000 mm2; 20,000 mm2; 30,000 mm2; 40,000 mm2; 50,000 mm2 or more. In some instances, the thickness is between about 50 mm and about 2000 mm. between about 50 mm and about 1000 mm, between about 100 mm and about 1000 mm, between about 200 mm and about 1000 mm, or between about 250 mm and about 1000 mm. Non-limiting examples thickness include 275 mm, 375 mm, 525 mm, 625 mm, 675 mm, 725 mm, 775 mm and 925 mm. In some instances, the thickness is at least or about 0.5 mm, 1.0 mm, 1.5 mm, 2.0 mm, 2.5 mm. 3.0 mm, 3.5 mm, 4.0 mm, or more than 4.0 mm. In some cases, the thickness of varies with diameter and depends on the composition of the substrate. For example, a structure comprising materials other than silicon may have a different thickness than a silicon structure of the same diameter. Structure thickness may be determined by the mechanical strength of the material used and the structure must be thick enough to support its own weight without cracking during handling. In some instances, a structure is more than about 1, 2, 3, 4, 5, 10, 15, 30, 40, 50 feet in any one dimension.

[0130] Materials

[0131] Provided herein are devices comprising a surface, wherein the surface is modified to support polynucleotide synthesis at predetermined locations and with a resulting low error rate, a low dropout rate, a high yield, and a high oligo representation. In some instances, surfaces of devices for polynucleotide synthesis provided herein are fabricated from a variety of materials capable of modification to support a de novo polynucleotide synthesis reaction. In some cases, the devices are sufficiently conductive, e.g., are able to form uniform electric fields across all or a portion of the devices. Devices described herein may comprise a flexible material. Exemplary flexible materials include, without limitation, modified nylon, unmodified nylon, nitrocellulose, and polypropylene. Devices described herein may comprise a rigid material. Exemplary rigid materials include, without limitation, glass, fuse silica, silicon, silicon dioxide, silicon nitride, plastics (for example, polytetrafluoroethylene, polypropylene, polystyrene, polycarbonate, and blends thereof, and metals (for example, gold, platinum). Devices disclosed herein may be fabricated from a material comprising silicon, polystyrene, agarose, dextran, cellulosic polymers, polyacrylamides, poly dimethylsiloxane (PDMS), glass, or any combination thereof. In someAttorney Docket No. 00415-0062-00304 cases, devices disclosed herein are manufactured with a combination of materials listed herein or any other suitable material known in the art.

[0132] Devices described herein may comprise material having a range of tensile strength. Exemplary materials having a range of tensile strengths include, but are not limited to, nylon (70 MPa), nitrocellulose (1.5 MPa), polypropylene (40 MPa), silicon (268 MPa), polystyrene (40 MPa), agarose (1-10 MPa), polyacrylamide (1-10 MPa), poly dimethylsiloxane (PDMS) (3.9- 10.8 MPa). Solid supports described herein can have a tensile strength from 1 to 300, 1 to 40, 1 to 10, 1 to 5, or 3 to 11 MPa. Solid supports described herein can have a tensile strength of about 1, 1.5, 2, 3. 4, 5, 6, 7, 8, 9, 10, 11, 20, 25, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 270. or more MPa. In some instances, a device descnbed herein comprises a solid support for polynucleotide synthesis that is in the form of a flexible material capable of being stored in a continuous loop or reel, such as a tape or flexible sheet.

[0133] Young's modulus measures the resistance of a material to elastic (recoverable) deformation under load. Exemplary materials having a range of Young's modulus stiffness include, but are not limited to, nylon (3 GPa), nitrocellulose ( 1 .5 GPa), polypropylene (2 GPa), silicon (150 GPa), polystyrene (3 GPa), agarose (1-10 GPa), polyacrylamide (1-10 GPa), polydimethylsiloxane (PDMS) (1-10 GPa). Solid supports described herein can have a Young's moduli from 1 to 500, 1 to 40, 1 to 10. 1 to 5, or 3 to 11 GPa. Solid supports described herein can have a Young’s moduli of about 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 25, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 400, 500 GPa, or more. As the relationship between flexibility and stiffness are inverse to each other, a flexible material has a low Young’s modulus and changes its shape considerably under load. In some instances, a solid support described herein has a surface with a flexibility of at least nylon.

[0134] In some cases, devices disclosed herein comprise a silicon dioxide base and a surface layer of silicon oxide. Alternatively, the devices may have a base of silicon oxide. Surface of the devices provided here may be textured, resulting in an increase overall surface area for polynucleotide synthesis. Devices disclosed herein in some instances comprise at least 5 %, 10%, 25%, 50%, 80%, 90%, 95%, or 99% silicon. Devices disclosed herein in some instances are fabricated from silicon on insulator (SOI) wafer.

[0135] The structure may be fabricated from a variety of materials, suitable for the methods and compositions of the invention described herein. In instances, the materials from which the substrates / solid supports of the comprising the invention are fabricated exhibit a low7level of polynucleotide binding. In some situations, material that are transparent to visible and / or UV light can be employed. Materials that are sufficiently conductive, e.g. those that can formAttorney Docket No. 00415-0062-00304 uniform electric fields across all or a portion of the substrates / solids support described herein, can be utilized. In some instances, such materials may be connected to an electric ground. In some cases, the substrate or solid support can be heat conductive or insulated. The materials can be chemical resistant and heat resistant to support chemical or biochemical reactions such as a series of polynucleotide synthesis reactions. For flexible materials, materials of interest include nylon, both modified and unmodified, nitrocellulose, polypropylene, and the like.

[0136] For rigid materials, specific materials of interest include glass; fuse silica; silicon, plastics (for example polytetrafluoroethylene, polypropylene, polystyrene, polycarbonate, and blends thereof, and the like); metals (for example, gold, platinum, and the like). The structure can be fabricated from a material selected from the group consisting of silicon, polystyrene, agarose, dextran, cellulosic polymers, polyacrylamides, polydimethylsiloxane (PDMS), and glass. The substrates / solid supports or the microstructures, reactors therein may be manufactured with a combination of materials listed herein or any other suitable material known in the art.

[0137] In some instances, a substrate disclosed herein comprises a computer readable material. Computer readable materials include, without limitation, magnetic media, reel-to-reel tape, cartridge tape, cassette tape, flexible disk, paper media, film, microfiche, continuous tape (e.g., a belt) and any media suitable for storing electronic instructions. In some cases, the substrate comprises magnetic reel-to-reel tape or a magnetic belt. In some instances, the substrate comprises a flexible printed circuit board.

[0138] Structures described herein may be transparent to visible and / or UV light. In some instances, structures described herein are sufficiently conductive to form uniform electric fields across all or a portion of a structure. In some instances, structures described herein are heat conductive or insulated. In some instances, the structures are chemical resistant and heat resistant to support a chemical reaction such as a polynucleotide synthesis reaction. In some instances, the substrate is magnetic. In some instances, the structures comprise a metal or a metal alloy.

[0139] Structures for polynucleotide synthesis may be over 1, 2, 5, 10, 30, 50 or more feet long in any dimension. In the case of a flexible structure, the flexible structure is optionally stored in a wound state, e.g., in a reel. In the case of a large rigid structure, e.g., greater than 1 foot in length, the rigid structure can be stored vertically or horizontally.

[0140] Surface Preparation

[0141] Provided herein are methods to support the immobilization of a biomolecule on a substrate, where a surface of a structure described herein comprises a material and / or is coated with a material that facilitates a coupling reaction with the biomolecule for attachment. ToAttorney Docket No. 00415-0062-00304 prepare a structure for biomolecule immobilization, surface modifications may be employed that chemically and / or physically alter the substrate surface by an additive or subtractive process to change one or more chemical and / or physical properties of a substrate surface or a selected site or region of the surface. For example, surface modification involves (1) changing the wetting properties of a surface. (2) functionalizing a surface, i.e. providing, modifying or substituting surface functional groups, (3) defunctionalizing a surface, i.e. removing surface functional groups, (4) otherwise altering the chemical composition of a surface, e.g., through etching, (5) increasing or decreasing surface roughness, (6) providing a coating on a surface, e.g., a coating that exhibits wetting properties that are different from the wetting properties of the surface, and / or (7) depositing particulates on a surface. In some instances, the surface of a structure is selectively functionalized to produce two or more distinct areas on a structure, wherein at least one area has a different surface or chemical property7that another area of the same structure. Such properties include, without limitation, surface energy, chemical termination, surface concentration of a chemical moiety, and the like.

[0142] In some instances, a surface of a structure disclosed herein is modified to comprise one or more actively functionalized surfaces configured to bind to both the surface of the substrate and a biomolecule, thereby supporting a coupling reaction to the surface. In some instances, the surface is also functionalized with a passive material that does not efficiently bind the biomolecule, thereby preventing biomolecule attachment at sites where the passive functionalization agent is bound. In some cases, the surface comprises an active layer only defining distinct loci for biomolecule support.

[0143] In some instances, the surface is contacted with a mixture of functionalization groups which are in any different ratio. In some instances, a mixture comprises at least 2, 3, 4. 5 or more different types of functionalization agents. In some cases, the ratio of the at least two types of surface functionalization agents in a mixture is about 1 :1, 1:2, 1 :5, 1: 10, 2: 10, 3: 10, 4: 10, 5: 10, 6: 10, 7: 10, 8: 10, 9:10, or any other ratio to achieve a desired surface representation of two groups. In some instances, desired surface tensions, wettabilities, water contact angles, and / or contact angles for other suitable solvents are achieved by providing a substrate surface with a suitable ratio of functionalization agents. In some cases, the agents in a mixture are chosen from suitable reactive and inert moieties, thus diluting the surface density' of reactive groups to a desired level for downstream reactions. In some instances, the mixture of functionalization reagents comprises one or more reagents that bind to a biomolecule and one or more reagents that do not bind to a biomolecule. Therefore, modulation of the reagents allows for the control of the amount of biomolecule binding that occurs at a distinct area of functionalization.Attorney Docket No. 00415-0062-00304

[0144] In some instances, a method for substrate functionalization comprises deposition of a silane molecule onto a surface of a substrate. The silane molecule may be deposited on a high energy surface of the substrate. In some instances the high surface energy' region includes a passive functionalization reagent. Methods described herein provide for a silane group to bind the surface, while the rest of the molecule provides a distance from the surface and a free hydroxyl group at the end to which a biomolecule attaches. In some instances, the silane is an organofunctional alkoxysilane molecule. Non-limiting examples of organofunctional alkoxysilane molecules include dimethylchloro-octodecyl-silane, methyldichloro-octodecyl- silane, trichloro-octodecyl-silane, and trimethyl-octodecyl-silane. triethyl-octodecyl-silane. In some instances, the silane is an amino silane. Examples of amino silanes include, without limitation, 11 -acetoxyundecyltri ethoxy silane, n-decyltriethoxysilane, (3- aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, gly ci dyloxypropyl / trimethoxy silane and N-(3-triethoxysilylpropyl)-4-hydroxybutyramide. In some instances, the silane comprises 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, glycidyloxypropyl / trimethoxysilane, N-(3-triethoxysilylpropyl)-4-hydroxybutyramide, or any combination thereof. In some instances, an active functionalization agent comprises 11- acetoxyundecyltriethoxysilane. In some instances, an active functionalization agent comprises n- decyltriethoxysilane. In some cases, an active functionalization agent comprises glycidyloxypropyltriethoxysilane (GOPS). In some instances, the silane is a fluorosilane. In some instances, the silane is a hydrocarbon silane. In some cases, the silane is 3-iodo- propyltrimethoxysilane. In some cases, the silane is oclylchlorosilane.

[0145] In some instances, silanization is performed on a surface through self-assembly with organofunctional alkoxysilane molecules. The organofunctional alkoxysilanes are classified according to their organic functions. Non-limiting examples of siloxane functionalizing reagents include hydroxyalkyl siloxanes (silylate surface, functionalizing with diborane and oxidizing the alcohol by hydrogen peroxide), diol (dihydroxyalkyl) siloxanes (silylate surface, and hydrolyzing to diol), aminoalkyl siloxanes (amines require no intermediate functionalizing step), glycidoxysilanes (3-glycidoxypropyl-dimethyl-ethoxysilane, glycidoxy-trimethoxysilane), mercaptosilanes (3-mercaptopropyl-trimethoxysilane, 3-4 epoxy cyclohexylethyltrimethoxysilane or 3-mercaptopropyl-methyl-dimethoxysilane), bicyclohepthenyl- trichlorosilane, butyl-aldehydr-trimethoxysilane, or dimeric secondary aminoalkyl siloxanes. Exemplary hydroxyalkyl siloxanes include allyl trichlorochlorosilane turning into 3- hydroxypropyl, or 7-oct-l-enyl trichlorochlorosilane turning into 8-hydroxy oct l. The diolAttorney Docket No. 00415-0062-00304(dihydroxyalkyl) siloxanes include glycidyl trimethoxysilane-derived (2.3- dihydroxypropyloxy)propyl (GOPS). The aminoalkyl siloxanes include 3-aminopropyl trimethoxysilane turning into 3-aminopropyl (3-aminopropyl-tnethoxysilane. 3-aminopropyl- diethoxy-methylsilane. 3-aminopropyl-dimethyl-ethoxysilane, or 3 -aminopropyltrimethoxysilane). In some cases, the dimeric secondary aminoalkyl siloxanes is bis (3- trimethoxysilylpropyl) amine turning into bis(silyloxylpropyl)amine.

[0146] Active functionalization areas may comprise one or more different species of silanes, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more silanes. In some cases, one of the one or more silanes is present in the functionalization composition in an amount greater than another silane. For example, a mixed silane solution having two silanes comprises a 99: 1, 98:2, 97:3, 96:4, 95:5, 94:6, 93:7, 92:8, 91 :9, 90: 10, 89: 11, 88: 12, 87: 13, 86: 14, 85: 15, 84:16, 83: 17, 82: 18, 81 : 19, 80:20, 75:25, 70:30, 65:35, 60:40, 55:45 ratio of one silane to another silane. In some instances, an active functionalization agent comprises 11 -acetoxy undecyltriethoxy silane and n- decyltri ethoxy silane. In some instances, an active functionalization agent comprises 11- acetoxyundecyltri ethoxysilane and n-decyltriethoxysilane in a ratio from about 20:80 to about 1:99, or about 10:90 to about 2:98, or about 5:95.

[0147] In some instances, functionalization comprises deposition of a functionalization agent to a structure by any deposition technique, including, but not limiting to, chemical vapor deposition (CVD), atomic layer deposition (ALD), plasma enhanced CVD (PECVD), plasma enhanced ALD (PEALD), metal organic CVD (MOCVD), hot wire CVD (HWCVD), initiated CVD (iCVD), modified CVD (MCVD), vapor axial deposition (VAD), outside vapor deposition (OVD), physical vapor deposition (e.g., sputter deposition, evaporative deposition), and molecular layer deposition (MLD).

[0148] Any step or component in the following functionalization process be omitted or changed in accordance with properties desired of the final functionalized substrate. In some cases, additional components and / or process steps are added to the process workflows embodied herein. In some instances, a substrate is first cleaned, for example, using a piranha solution. An example of a cleaning process includes soaking a substrate in a piranha solution (e.g., 90% H2SO4, 10% H2O2) at an elevated temperature (e.g., 120 °C) and washing (e.g., water) and drying the substrate (e.g., nitrogen gas). The process optionally includes a post piranha treatment comprising soaking the piranha treated substrate in a basic solution (e.g., NH4OH) followed by an aqueous wash (e.g., water). In some instances, a surface of a structure is plasma cleaned, optionally following the piranha soak and optional post piranha treatment. An example of a plasma cleaning process comprises an oxygen plasma etch. In some instances, the surface isAttorney Docket No. 00415-0062-00304 deposited with an active functionalization agent following by vaporization. In some instances, the substrate is actively functionalized prior to cleaning, for example, by piranha treatment and / or plasma cleaning.

[0149] The process for surface functionalization optionally comprises a resist coat and a resist strip. In some instances, following active surface functionalization, the substrate is spin coated with a resist, for example, SPR™ 3612 positive photoresist. The process for surface functionalization, in various instances, comprises lithography with patterned functionalization. In some instances, photolithography is performed following resist coating. In some instances, after lithography, the surface is visually inspected for lithography defects. The process for surface functionalization, in some instances, comprises a cleaning step, whereby residues of the substrate are removed, for example, by plasma cleaning or etching. In some instances, the plasma cleaning step is performed at some step after the lithography step.

[0150] In some instances, a surface coated with a resist is treated to remove the resist, for example, after functionalization and / or after lithography. In some cases, the resist is removed with a solvent, for example, with a stripping solution comprising N-methyl-2-pyrrolidone. In some cases, resist stripping comprises sonication or ultrasonication. In some instances, a resist is coated and stripped, followed by active functionalization of the exposed areas to create a desired differential functionalization pattern.

[0151] In some instances, the methods and compositions described herein relate to the application of photoresist for the generation of modified surface properties in selective areas, wherein the application of the photoresist relies on the fluidic properties of the surface defining the spatial distribution of the photoresist. Without being bound by theory, surface tension effects related to the applied fluid may define the flow of the photoresist. For example, surface tension and / or capillary action effects may facilitate drawing of the photoresist into small structures in a controlled fashion before the resist solvents evaporate. In some instances, resist contact points are pinned by sharp edges, thereby controlling the advance of the fluid. The underlying structures may be designed based on the desired flow patterns that are used to apply photoresist during the manufacturing and functionalization processes. A solid organic layer left behind after solvents evaporate may be used to pursue the subsequent steps of the manufacturing process. Structures may be designed to control the flow of fluids by facilitating or inhibiting wicking effects into neighboring fluidic paths. For example, a structure is designed to avoid overlap between top and bottom edges, which facilitates the keeping of the fluid in top structures allowing for a particular disposition of the resist. In an alternative example, the top and bottom edges overlap, leading to the wicking of the applied fluid into bottom structures. AppropriateAttorney Docket No. 00415-0062-00304 designs may be selected accordingly, depending on the desired application of the resist.

[0152] In some instances, a structure described herein has a surface that comprises a material having thickness of at least or at least 0. 1 nm, 0.5 nm, 1 nm, 2 nm, 5 nm, 10 nm or 25 nm that comprises a reactive group capable of binding nucleosides. Exemplary include, without limitation, glass and silicon, such as silicon dioxide and silicon nitride. In some cases, exemplary surfaces include nylon and PMMA.

[0153] In some instances, electromagnetic radiation in the form of UV light is used for surface patterning. In some instances, a lamp is used for surface patterning, and a mask mediates exposure locations of the UV light to the surface. In some instances, a laser is used for surface patterning, and a shutter opened / closed state controls exposure of the UV light to the surface. The laser arrangement may be used in combination with a flexible structure that is capable of moving. In such an arrangement, the coordination of laser exposure and flexible structure movement is used to create patterns of one or more agents having differing nucleoside coupling capabilities.

[0154] Described herein are surfaces for polynucleotide synthesis that are reusable. After synthesis and / or cleavage of polynucleotides, a surface may be bathed, washed, cleaned, baked, etched, or otherwise functionally restored to a condition suitable for subsequent polynucleotide synthesis. The number of times a surface is reused and the methods for recycling / preparing the surface for reuse vary depending on subsequent applications. Surfaces prepared for reuse are in some instances reused at least 1, 2, 3, 5, 10, 20, 50, 100, 1,000 or more times. In some instances, the remaining “life” or number of times a surface is suitable for reuse is measured or predicted.

[0155] De Novo Polynucleotide Synthesis

[0156] Provided herein are systems and methods for synthesis of a high density of polynucleotides on a substrate in a short amount of time. In some instances, the substrate is a flexible substrate. In some instances, at least 1010, 1011, 1012, 101?, 1014, or 1015bases are synthesized in one day. In some instances, at least 10 x 108, 10 x 109, 10 x 1010, 10 x 1011, or 10 x 1012polynucleotides are synthesized in one day. In some cases, each polynucleotide synthesized comprises at least 20, 25, 50, 100, 200, 300, 400 or at least 500 nucleobases. In some cases, each polynucleotide synthesized comprises 20-500, 25-500, 50-500, 100-500, 200- 500, 300-500, 400-500 50-250, 50-300, 100-300, or 150-400 bases. In some cases, these bases are synthesized with a total average error rate of less than about 1 in 100; 200; 300; 400; 500; 1000; 2000; 5000; 10000; 15000; 20000 bases. In some instances, these error rates are for at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5%, or more of the polynucleotides synthesized. In some instances, these at least 90%, 95%, 98%, 99%, 99.5%, or more of theAttorney Docket No. 00415-0062-00304 polynucleotides synthesized do not differ from a predetermined sequence for which they encode. In some instances, the error rate for synthesized polynucleotides on a substrate using the methods and systems described herein is less than about 1 in 200. In some instances, the error rate for synthesized polynucleotides on a substrate using the methods and systems described herein is less than about 1 in 1,000. In some instances, the error rate for synthesized polynucleotides on a substrate using the methods and systems described herein is less than about 1 in 2,000. In some instances, the error rate for synthesized polynucleotides on a substrate using the methods and systems described herein is less than about 1 in 3,000. In some instances, the error rate for synthesized polynucleotides on a substrate using the methods and systems described herein is less than about 1 in 5,000. Individual types of error rates include mismatches, deletions, insertions, and / or substitutions for the polynucleotides synthesized on the substrate. The term “error rate” refers to a comparison of the collective amount of synthesized polynucleotide to an aggregate of predetermined polynucleotide sequences. In some instances, synthesized polynucleotides disclosed herein comprise a tether of 12 to 25 bases. In some instances, the tether comprises 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more bases.

[0157] Described herein are methods, systems, devices, and compositions wherein chemical reactions used in polynucleotide synthesis are controlled using electrochemistry. Electrochemical reactions in some instances are controlled by any source of energy, such as light, heat, radiation, or electricity. For example, electrodes are used to control chemical reactions as all or a portion of discrete loci on a surface. Electrodes in some instances are charged by applying an electrical potential to the electrode to control one or more chemical steps in polynucleotide synthesis. In some instances, these electrodes are addressable. Any number of the chemical steps described herein is in some instances controlled with one or more electrodes. Electrochemical reactions may comprise oxidations, reductions, acid / base chemistry, or other reaction that is controlled by an electrode. In some instances, electrodes generate electrons or protons that are used as reagents for chemical transformations. Electrodes in some instances directly generate a reagent such as an acid. In some instances, an acid is a proton. Electrodes in some instances directly generate a reagent such as a base. Acids or bases are often used to cleave protecting groups, or influence the kinetics of various polynucleotide synthesis reactions, for example by adjusting the pH of a reaction solution. Electrochemically controlled polynucleotide synthesis reactions in some instances comprise redox-active metals or other redox-active organic materials. In some instances, metal or organic catalysts are employed with these electrochemicalAttorney Docket No. 00415-0062-00304 reactions. In some instances, acids are generated from oxidation of quinones.

[0158] Control of chemical reactions with is not limited to the electrochemical generation of reagents; chemical reactivity' may be influenced indirectly through biophysical changes to substrates or reagents through electric fields (or gradients) which are generated by electrodes. In some instances, substrates include but are not limited to nucleic acids. In some instances, electrical fields which repel or attract specific reagents or substrates towards or away from an electrode or surface are generated. Such fields in some instances are generated by application of an electrical potential to one or more electrodes. For example, negatively charged nucleic acids are repelled from negatively charged electrode surfaces. Such repulsions or attractions of polynucleotides or other reagents caused by local electric fields in some instances provides for movement of polynucleotides or other reagents in or out of region of the synthesis device or structure. In some instances, electrodes generate electric fields which repel polynucleotides away from a synthesis surface, structure, or device. In some instances, electrodes generate electric fields which attract polynucleotides towards a synthesis surface, structure, or device. In some instances, protons are repelled from a positively charged surface to limit contact of protons with substrates or portions thereof. In some instances, repulsion or attractive forces are used to allow or block entry' of reagents or substrates to specific areas of the synthesis surface. In some instances, nucleoside monomers are prevented from contacting a polynucleotide chain byapplication of an electric field in the vicinity of one or both components. Such arrangements allow gating of specific reagents, which may obviate the need for protecting groups when the concentration or rate of contact between reagents and / or substrates is controlled. In some instances, unprotected nucleoside monomers are used for polynucleotide synthesis.Alternatively, application of the field in the vicinity of one or both components promotes contact of nucleoside monomers with a polynucleotide chain. Additionally, application of electric fields to a substrate can alter the substrates reactivity' or conformation. In an exemplary' application, electric fields generated by electrodes are used to prevent polynucleotides at adjacent loci from interacting. In some instances, the substrate is a polynucleotide, optionally attached to a surface. Application of an electric field in some instances alters the three-dimensional structure of a polynucleotide. Such alterations comprise folding or unfolding of various structures, such as helices, hairpins, loops, or other 3-dimensional nucleic acid structure. Such alterations are useful for manipulating nucleic acids inside of wells, channels, or other structures. In some instances, electric fields are applied to a nucleic acid substrate to prevent secondary structures. In some instances, electric fields obviate the need for linkers or attachment to a solid support during polynucleotide synthesis.Attorney Docket No. 00415-0062-00304

[0159] A suitable method for polynucleotide synthesis on a substrate of this disclosure is a phosphoramidite method comprising the controlled addition of a phosphoramidite building block, i.e. nucleoside phosphoramidite, to a growing polynucleotide chain in a coupling step that forms a phosphite triester linkage betw een the phosphoramidite building block and a nucleoside bound to the substrate. In some instances, the nucleoside phosphoramidite is provided to the substrate activated. In some instances, the nucleoside phosphoramidite is provided to the substrate with an activator. In some instances, nucleoside phosphoramidites are provided to the substrate in a 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17. 18, 19, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100-fold excess or more over the substrate-bound nucleosides. In some instances, the addition of nucleoside phosphoramidite is performed in an anhydrous environment, for example, in anhydrous acetonitrile. Following addition and linkage of a nucleoside phosphoramidite in the coupling step, the substrate is optionally washed. In some instances, the coupling step is repeated one or more additional times, optionally with a wash step between nucleoside phosphoramidite additions to the substrate. In some instances, a polynucleotide synthesis method used herein comprises 1 , 2, 3 or more sequential coupling steps. Prior to coupling, in many cases, the nucleoside bound to the substrate is de-protected by removal of a protecting group, where the protecting group functions to prevent polymerization. Protecting groups may comprise any chemical group that prevents extension of the polynucleotide chain. In some instances, the protecting group is cleaved (or removed) in the presence of an acid. In some instances, the protecting group is cleaved in the presence of a base. In some instances, the protecting group is removed with electromagnetic radiation such as light, heat, or other energy source. In some instances, the protecting group is removed through an oxidation or reduction reaction. In some instances, a protecting group comprises a triarylmethyl group. In some instances, a protecting group comprises an aryl ether. In some instances, a protecting comprises a disulfide. In some instances a protecting group comprises an acid-labile silane. In some instances, a protecting group comprises an acetal. In some instances, a protecting group comprises a ketal. In some instances, a protecting group comprises an enol ether. In some instances, a protecting group comprises a methoxybenzyl group. In some instances, a protecting group comprises an azide. In some instances, a protecting group is 4,4 ’-dimeth oxy trityl (DMT). In some instances, a protecting group is an DMT-aminooxyl protecting group. In some instances, a protecting group is a quinone oxime protecting group. In some instances, a protecting group is a tert-butyl carbonate. In some instances, a protecting group is a tert-butyl ester. In some instances, a protecting group comprises a base-labile group.

[0160] Following coupling, phosphoramidite polynucleotide synthesis methods optionallyAttorney Docket No. 00415-0062-00304 comprise a capping step. In a capping step, the growing polynucleotide is treated with a capping agent. A capping step generally serves to block unreacted substrate-bound 5 ’-OH groups after coupling from further chain elongation, preventing the formation of polynucleotides with internal base deletions. Further, phosphoramidites activated with IH-tetrazole often react, to a small extent, with the 06 position of guanosine. Without being bound by theory, upon oxidation with h / water, this side product, possibly via O6-N7 migration, undergoes depurination. The apurinic sites can end up being cleaved in the course of the final deprotection of the polynucleotide thus reducing the yield of the full-length product. The 06 modifications may be removed by treatment with the capping reagent prior to oxidation with I2 / water. In some instances, inclusion of a capping step during polynucleotide synthesis decreases the error rate as compared to synthesis without capping. As an example, the capping step comprises treating the substrate-bound polynucleotide with a mixture of acetic anhydride and 1 -methylimidazole. Following a capping step, the substrate is optionally ashed.

[0161] Following addition of a nucleoside phosphoramidite, and optionally after capping and one or more wash steps, a substrate described herein comprises a bound growing nucleic acid that may be oxidized. The oxidation step comprises oxidizing the phosphite triester into a tetracoordinated phosphate triester, a protected precursor of the naturally occurring phosphate diester intemucleoside linkage. In some instances, phosphite triesters are oxidized electrochemically. In some instances, oxidation of the growing polynucleotide is achieved by treatment with iodine and water, optionally in the presence of a weak base such as a pyridine, lutidine, or collidine. Oxidation is sometimes carried out under anhydrous conditions using tert- Butyl hydroperoxide or (lS)-(+)-(10-camphorsulfonyl)-oxaziridine (CSO). In some methods, a capping step is performed following oxidation. A second capping step allows for substrate drying, as residual w ater from oxidation that may persist can inhibit subsequent coupling. Following oxidation, the substrate and growing polynucleotide is optionally washed. In some instances, the step of oxidation is substituted with a sulfurization step to obtain polynucleotide phosphorothioates. wherein any capping steps can be performed after the sulfurization. Many reagents are capable of the efficient sulfur transfer, including, but not limited to, 3-(Dimethy laminomethylidene)amino)-3H- 1 ,2,4-dithiazole-3 -thione, DDTT, 3H- 1 ,2-benzodithi 01- 3-one 1,1-dioxide, also known as Beaucage reagent, and N,N,N'N'-Tetraethylthiuram disulfide (TETD).

[0162] For a subsequent cycle of nucleoside incorporation to occur through coupling, a protected 5’ end (or 3’ end, if synthesis is conducted in a 5’ to 3’ direction) of the substrate bound growing polynucleotide is be removed so that the primary7hydroxyl group can react withAttorney Docket No. 00415-0062-00304 a next nucleoside phosphoramidite. In some instances, the protecting group is DMT and deblocking occurs with an acid. In some instances, the protecting group is DMT and deblocking occurs with electrochemically generated protons. Deblocking in some instances occurs in the presence of auxiliary reagents which can accept or donate electrons (e.g., methylene blue). Conducting detritylation for an extended time or with stronger than recommended solutions of acids may lead to increased depurination of solid support-bound polynucleotide and thus reduces the yield of the desired full-length product. Methods and compositions described herein provide for controlled deblocking conditions limiting undesired depurination reactions. In some instances, the substrate bound polynucleotide is washed after deblocking. In some cases, efficient washing after deblocking contributes to synthesized polynucleotides having a low error rate.

[0013] Methods for the synthesis of polynucleotides on a substrate described herein may involve an iterating sequence of the following steps: application of a protected monomer to a surface of a substrate feature to link with either the surface, a linker or with a previously deprotected monomer; deprotection of the applied monomer so that it can react with a subsequently applied protected monomer; and application of another protected monomer for linking. One or more intermediate steps include oxidation and / or sulfurization. In some instances, one or more w ash steps precede or follow one or all of the steps.

[0164] Methods for the synthesis of polynucleotides on a substrate described herein may comprise an oxidation step. For example, methods involve an iterating sequence of the following steps: application of a protected monomer to a surface of a substrate feature to link with either the surface, a linker or with a previously deprotected monomer; deprotection of the applied monomer so that it can react with a subsequently applied protected monomer; application of another protected monomer for linking, and oxidation and / or sulfurization. In some instances, one or more wash steps precede or follow7one or all of the steps.

[0165] Methods for the synthesis of polynucleotides on a substrate described herein may further comprise an iterating sequence of the following steps: application of a protected monomer to a surface of a substrate feature to link with either the surface, a linker or with a previously deprotected monomer; deprotection of the applied monomer so that it can react with a subsequently applied protected monomer; and oxidation and / or sulfurization. In some instances, one or more wash steps precede or follow one or all of the steps.

[0166] Methods for the synthesis of polynucleotides on a substrate described herein may further comprise an iterating sequence of the following steps: application of a protected monomer to a surface of a substrate feature to link with either the surface, a linker or with a previouslyAttorney Docket No. 00415-0062-00304 deprotected monomer; and oxidation and / or sulfurization. In some instances, one or more wash steps precede or follow one or all of the steps.

[0017] Methods for the synthesis of polynucleotides on a substrate described herein may further comprise an iterating sequence of the following steps: application of a protected monomer to a surface of a substrate feature to link with either the surface, a linker or with a previously deprotected monomer; deprotection of the applied monomer so that it can react with a subsequently applied protected monomer; and oxidation and / or sulfurization. In some instances, one or more wash steps precede or follow one or all of the steps.

[0168] In some instances, polynucleotides are synthesized with photolabile protecting groups, where the hydroxyl groups generated on the surface are blocked by photolabile-protecting groups. When the surface is exposed to UV light, such as through a photolithographic mask, a pattern of free hydroxyl groups on the surface may be generated. These hydroxyl groups can react with photoprotected nucleoside phosphoramidites. according to phosphoramidite chemistry. A second photolithographic mask can be applied and the surface can be exposed to UV light to generate second pattern of hydroxyl groups, followed by coupling with 5'- photoprotected nucleoside phosphoramidite. Likewise, patterns can be generated and oligomer chains can be extended. Without being bound by theory, the lability of a photocleavable group depends on the wavelength and polarity of a solvent employed and the rate of photocleavage may be affected by the duration of exposure and the intensity of light. This method can leverage a number of factors such as accuracy in alignment of the masks, efficiency of removal of photoprotecting groups, and the yields of the phosphoramidite coupling step. Further, unintended leakage of light into neighboring sites can be minimized. The density of synthesized oligomer per spot can be monitored by adjusting loading of the leader nucleoside on the surface of synthesis.

[0019] The surface of a substrate described herein that provides support for polynucleotide synthesis may be chemically modified to allow for the synthesized polynucleotide chain to be cleaved from the surface. In some instances, the polynucleotide chain is cleaved at the same time as the polynucleotide is deprotected. In some cases, the polynucleotide chain is cleaved after the polynucleotide is deprotected. In an exemplary scheme, a trialkoxysilyl amine such as (CH3CH2O)3Si-(CH2)2-NH2 is reacted with surface SiOH groups of a substrate, followed byreaction with succinic anhydride with the amine to create an amide linkage and a free OH on which the nucleic acid chain growth is supported. Cleavage includes gas cleavage with ammonia or methylamine. In some instances cleavage includes linker cleavage with electrically generated reagents such as acids or bases. In some instances, once released from the surface,Attorney Docket No. 00415-0062-00304 polynucleotides are assembled into larger nucleic acids that are sequenced and decoded to extract stored information.

[0170] The surfaces described herein can be reused after polynucleotide cleavage to support additional cycles of polynucleotide synthesis. For example, the linker can be reused without additional treatment / chemical modifications. In some instances, a linker is non-covalently bound to a substrate surface or a polynucleotide. In some embodiments, the linker remains attached to the polynucleotide after cleavage from the surface. Linkers in some embodiments comprise reversible covalent bonds such as esters, amides, ketals, beta substituted ketones, heterocycles, or other group that is capable of being reversibly cleaved. Such reversible cleavage reactions are in some instances controlled through the addition or removal of reagents, or by electrochemical processes controlled by electrodes. Optionally, chemical linkers or surface-bound chemical groups are regenerated after a number of cycles, to restore reactivity7and remove unwanted side product formation on such linkers or surface-bound chemical groups.

[0171] Assembly

[0172] Polynucleotides may be designed to collectively span a large region of a predetermined sequence that encodes for information. In some instances, larger polynucleotides are generated through ligation reactions to join the synthesized polynucleotides. One example of a ligation reaction is polymerase chain assembly (PCA). In some instances, at least of a portion of the polynucleotides are designed to include an appended region that is a substrate for universal primer binding. For PCA reactions, the presynthesized polynucleotides include overlaps with each other (e g., 4, 20, 40 or more bases with overlapping sequence). During the polymerase cycles, the polynucleotides anneal to complementary fragments and then are filled in by polymerase. Each cycle thus increases the length of various fragments randomly depending on which polynucleotides find each other. Complementarity amongst the fragments allows for forming a complete large span of double-stranded DNA. In some cases, after the PCA reaction is complete, an error correction step is conducted using mismatch repair detecting enzymes to remove mismatches in the sequence. Once larger fragments of a target sequence are generated, they can be amplified. For example, in some cases, a target sequence comprising 5’ and 3’ terminal adapter sequences is amplified in a polymerase chain reaction (PCR) which includes modified primers that hybridize to the adapter sequences. In some cases, the modified primers comprise one or more uracil bases. The use of modified primers allows for removal of the primers through enzymatic reactions centered on targeting the modified base and / or gaps left by enzymes which cleave the modified base pair from the fragment. What remains is a doublestranded amplification product that lacks remnants of adapter sequence. In this way, multipleAttorney Docket No. 00415-0062-00304 amplification products can be generated in parallel with the same set of primers to generate different fragments of double-stranded DNA.

[0173] Error correction may be performed on synthesized polynucleotides and / or assembled products. An example strategy for error correction involves site-directed mutagenesis by overlap extension PCR to correct errors, which is optionally coupled with two or more rounds of cloning and sequencing. In certain instances, double-stranded nucleic acids with mismatches, bulges and small loops, chemically altered bases and / or other heteroduplexes are selectively removed from populations of correctly synthesized nucleic acids. In some instances, error correction is performed using proteins / enzymes that recognize and bind to or next to mismatched or unpaired bases within double-stranded nucleic acids to create a single or double-strand break or to initiate a strand transfer transposition event. Non-limiting examples of proteins / enzymes for error correction include endonucleases (T7 Endonuclease I, E. coli Endonuclease V, T4 Endonuclease VII, mung bean nuclease, Cell, E. coli Endonuclease IV, UVDE). restriction enzymes, glycosylases. ribonucleases, mismatch repair enzymes, resolvases, helicases, ligases, antibodies specific for mismatches, and their variants. Examples of specific error correction enzymes include T4 endonuclease 7, T7 endonuclease 1, SI, mung bean endonuclease, MutY, MutS, MutH, MutL, cleavase, CELI, and HINF1. In some cases, DNA mismatch-binding protein MutS (Thermus aquaticus) is used to remove failure products from a population of synthesized products. In some instances, error correction is performed using the enzyme Correctase. In some cases, error correction is performed using SURVEYOR endonuclease (Transgenomic), a mismatch-specific DNA endonuclease that scans for known and unknown mutations and polymorphisms for heteroduplex DNA.

[0174] Sequencing

[0175] After extraction and / or amplification of polynucleotides from the surface of the structure, suitable sequencing technology7may be employed to sequence the polynucleotides. In some cases, the DNA sequence is read on the substrate or within a feature of a structure. In some cases, the polynucleotides stored on the substrate are extracted is optionally assembled into longer nucleic acids and then sequenced.

[0176] Polynucleotides synthesized and stored on the structures described herein encode data that can be interpreted by reading the sequence of the synthesized polynucleotides and converting the sequence into binary code readable by a computer. In some cases the sequences require assembly, and the assembly step may need to be at the nucleic acid sequence stage or at the digital sequence stage.

[0177] Provided herein are detection systems comprising a device capable of sequencing storedAttorney Docket No. 00415-0062-00304 polynucleotides, either directly on the structure and / or after removal from the main structure. In cases where the structure is a reel-to-reel tape of flexible material, the detection system comprises a device for holding and advancing the structure through a detection location and a detector disposed proximate the detection location for detecting a signal originated from a section of the tape when the section is at the detection location. In some instances, the signal is indicative of a presence of a polynucleotide. In some instances, the signal is indicative of a sequence of a polynucleotide (e.g., a fluorescent signal). In some instances, information encoded within polynucleotides on a continuous tape is read by a computer as the tape is conveyed continuously through a detector operably connected to the computer. In some instances, a detection system comprises a computer system comprising a polynucleotide sequencing device, a database for storage and retrieval of data relating to polynucleotide sequence, software for converting DNA code of a polynucleotide sequence to binary' code, a computer for reading the binary code, or any combination thereof.

[0178] Provided herein are sequencing systems that can be integrated into the devices described herein. Various methods of sequencing are well known in the art, and comprise “base calling” wherein the identity of a base in the target polynucleotide is identified. In some instances, polynucleotides synthesized using the methods, devices, compositions, and systems described herein are sequenced after cleavage from the synthesis surface. In some instances, sequencing occurs during or simultaneously with polynucleotide synthesis, wherein base calling occurs immediately after or before extension of a nucleoside monomer into the growing polynucleotide chain. Methods for base calling include measurement of electrical currents / voltages generated by polymerase-catalyzed addition of bases to a template strand. In some instances, synthesis surfaces comprise enzymes, such as polymerases. In some instances, such enzymes are tethered to electrodes or to the synthesis surface.

[0179] Computing Systems

[0180] In various aspects, any of the systems described herein are operably linked to a computer and are optionally automated through a computer either locally or remotely. In various instances, the methods and systems of the invention further comprise software programs on computer systems and use thereof. Accordingly, computerized control for the synchronization of the dispense / vacuum / refill functions such as orchestrating and synchronizing the material deposition device movement, dispense action and vacuum actuation are within the bounds of the invention. In some instances, the computer systems are programmed to interface between the user specified base sequence and the position of a material deposition device to deliver the correct reagents to specified regions of the substrate.Attorney Docket No. 00415-0062-00304

[0181] The computer system 3700 illustrated in FIG. 15A may be understood as a logical apparatus that can read instructions from media 3711 and / or a network port 3705, which can optionally be connected to server 3709 having fixed media 3712. The system can include a CPU 3701, disk drives 3703, optional input devices such as keyboard 3715 and / or mouse 3716 and optional monitor 3707. Data communication can be achieved through the indicated communication medium to a server at a local or a remote location. The communication medium can include any means of transmitting and / or receiving data. For example, the communication medium can be a network connection, a wireless connection or an internet connection. Such a connection can provide for communication over the World Wide Web. It is envisioned that data relating to the present disclosure can be transmitted over such networks or connections for reception and / or review by a party 3722.

[0182] FIG. 15B is a block diagram illustrating a first example architecture of a computer system that can be used in connection with example instances of the present invention. As depicted in FIG. 15B, the example computer system can include a processor 3802 for processing instructions. Non-limiting examples of processors include: Intel XeonTM processor, AMD OpteronTM processor, Samsung 32-bit RISC ARM 1176JZ(F)-S vl.OTM processor, ARM Cortex-A8 Samsung S5PC100TM processor, ARM Cortex-A8 Apple A4TM processor, Marvell PXA 930TM processor, or a functionally-equivalent processor. Multiple threads of execution can be used for parallel processing. In some instances, multiple processors or processors with multiple cores can also be used, whether in a single computer system, in a cluster, or distributed across systems over a network comprising a plurality7of computers, cell phones, and / or personal data assistant devices. As illustrated in FIG. 15B, a high speed cache 3804 can be connected to, or incorporated in. the processor 3802 to provide a high speed memory for instructions or data that have been recently, or are frequently, used by7processor 3802. The processor 3802 is connected to a north bridge 3806 by a processor bus 3808. The north bridge 3806 is connected to random access memory7(RAM) 3810 by a memory bus 3812 and manages access to the RAM 3810 by the processor 3802. The north bridge 3806 is also connected to a south bridge 3814 by a chipset bus 3816. The south bridge 3814 is, in turn, connected to a peripheral bus 3818. The peripheral bus can be, for example, PCI, PCI-X, PCI Express, or other peripheral bus. The north bridge and south bridge are often referred to as a processor chipset and manage data transfer between the processor. RAM, and peripheral components on the peripheral bus 3818. In some alternative architectures, the functionality of the north bridge can be incorporated into the processor instead of using a separate north bridge chip. In some instances, a system 3800 can include an accelerator card 3822 attached to the peripheral bus 3818. The accelerator can includeAttorney Docket No. 00415-0062-00304 field programmable gate arrays (FPGAs) or other hardware for accelerating certain processing. For example, an accelerator can be used for adaptive data restructuring or to evaluate algebraic expressions used in extended set processing.

[0183] Software and data are stored in external storage 3824 and can be loaded into RAM 3810 and / or cache 3804 for use by the processor. The system 3800 includes an operating system for managing system resources; non-limiting examples of operating systems include: Linux, Windows TM, MACOSTM, BlackBerry OSTM, iOSTM, and other functionally-equivalent operating systems, as well as application software running on top of the operating system for managing data storage and optimization in accordance with example embodiments of the present invention. In this example, system 3800 also includes network interface cards (NICs) 3820 and 3821 connected to the peripheral bus for providing network interfaces to external storage, such as Network Attached Storage (NAS) and other computer systems that can be used for distributed parallel processing.

[0184] FIG. 15C is a diagram showing a network 3900 with a plurality of computer systems 3902a, and 3902b, a plurality of cell phones and personal data assistants 3902c, and Network Attached Storage (NAS) 3904a, and 3904b. In example embodiments, systems 3902a, 3902b, and 3902c can manage data storage and optimize data access for data stored in Network Attached Storage (NAS) 3904a and 3904b. A mathematical model can be used for the data and be evaluated using distributed parallel processing across computer systems 3902a, and 3902b, and cell phone and personal data assistant systems 3902c. Computer systems 3902a, and 3902b, and cell phone and personal data assistant systems 3902c can also provide parallel processing for adaptive data restructuring of the data stored in Network Attached Storage (NAS) 3904a and 3904b. FIG. 4C illustrates an example only, and a wide variety of other computer architectures and systems can be used in conjunction with the various embodiments of the present invention. For example, a blade server can be used to provide parallel processing. Processor blades can be connected through a back plane to provide parallel processing. Storage can also be connected to the back plane or as Network Attached Storage (NAS) through a separate network interface.

[0185] In some example embodiments, processors can maintain separate memory spaces and transmit data through network interfaces, back plane or other connectors for parallel processing by other processors. In other embodiments, some or all of the processors can use a shared virtual address memory space. FIG. 15D is a block diagram of a multiprocessor computer system 4000 using a shared virtual address memory space in accordance with an example embodiment. The system includes a plurality of processors 4002a-f that can access a shared memory subsystem 4004. The system incorporates a plurality of programmable hardware memory algorithmAttorney Docket No. 00415-0062-00304 processors (MAPs) 4006a-f in the memory subsystem 4004. Each MAP 4006a-f can comprise a memory 4008a-f and one or more field programmable gate arrays (FPGAs) 4010a-f. The MAP provides a configurable functional unit and particular algorithms or portions of algorithms can be provided to the FPGAs 4010a-f for processing in close coordination with a respective processor. For example, the MAPs can be used to evaluate algebraic expressions regarding the data model and to perform adaptive data restructuring in example embodiments. In this example, each MAP is globally accessible by all of the processors for these purposes. In one configuration, each MAP can use Direct Memory Access (DMA) to access an associated memory 4008a-f, allowing it to execute tasks independently of. and asynchronously from, the respective microprocessor 4002a-f. In this configuration, a MAP can feed results directly to another MAP for pipelining and parallel execution of algorithms.

[0186] The above computer architectures and systems are examples only, and a wide variety' of other computer, cell phone, and personal data assistant architectures and systems can be used in connection with example embodiments, including systems using any combination of general processors, co-processors, FPGAs and other programmable logic devices, system on chips (SOCs), application specific integrated circuits (ASICs), and other processing and logic elements. In some embodiments, all or part of the computer system can be implemented in software or hardware. Any variety of data storage media can be used in connection with example embodiments, including random access memory, hard drives, flash memory, tape drives, disk arrays, Network Attached Storage (NAS) and other local or distributed data storage devices and systems.

[0187] In example embodiments, the computer system can be implemented using software modules executing on any of the above or other computer architectures and systems. In other embodiments, the functions of the system can be implemented partially or completely in firmware, programmable logic devices such as field programmable gate arrays (FPGAs), system on chips (SOCs). application specific integrated circuits (ASICs), or other processing and logic elements. For example, the Set Processor and Optimizer can be implemented with hardware acceleration through the use of a hardware accelerator card.EXAMPLES

[0188] The following illustrative examples are representative of embodiments of the software applications, systems, and methods described herein and are not meant to be limiting in any way.Example 1 - DNA Synthesis Using Dimethoxytrityl-aminooxyl as a Protecting Group

[0189] A surrogate phosphoramidite N (10-[N-Dimethoxytrityl-aminooxyethyl)]-Attorney Docket No. 00415-0062-00304 triethyleneglycol-l-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite) was used to evaluate the potency of deblocking this protecting group (e.g., FIG. 3).

[0190] An appropriate electrochemical deblocking solution was designed and optimized first to enable electrochemical deblocking process (“e-deblocking’"). A 5 -TTTTTTTTTTLLT-3' was firstly prepared on a silicon surface of a chip following an organic solvent electrochemical deblocking synthesis procedure with the aid of K&A synthesizer. Then amidite N was attached on the 5’ end under the same synthetic routine but without any capping subroutine to prevent formation of acetylated amine in this cycle. A 5’-DMT-NH-NTTTTTTTTTTLLT was obtained and ready to engage in electrochemical deblocking conditions. A variety of e-deblocking solutions were tested under different potentials to perform the removal of DMT-aminooxyl moiety. After deblocking, the DMT group on remaining DMT-aminoxyl oligos were washed away by trichloroacetic acid (TCA) solution, followed by aminooxyl acety lation via capping subroutine. The purpose of aminooxyl capping was because the aminooxyl group was labile and failed to survive downstream, as well as for the characterization processes; meanwhile an acetylated aminooxyl product showed greater stability’ and was identified by LCMS. The deblocking efficiency was revealed by comparing the ratio of deblocked NT10 and acetyl at ed- aminooxyl-NTlO. This was achieved after methylamine gas phase cleavage and deprotection, extraction and LC-mass spectroscopy processes.

[0191] Several aqueous e-deblock solutions were evaluated. A 5’-DMT protected oligo deblocking was examined first with e-deblock solution ESV3 and almost no signals of DMT removal could be found under aqueous e-deblock solution atmosphere. In contrast, the same ESV3 solution led to 48% to 77% deblocking rates in DMT-aminooxyl cases. Further optimization of e-deblock solutions successfully pushed deblocking efficiency up to 97%.

[0192] A spactioselective electrochemical deblocking process was demonstrated as well to prove the potential of synthesizing multiple oligos on single chip. 5’-DMT-NH- NTTTTTTTTTTLLT was prepared using the same protocol described above. Next, a selected region of the chip was switched-on to perform e-deblocking reaction followed by coupling of the next amidite. The deblocking and coupling steps were repeated until four different regions were coupled with A, C, G, T amidite respectively followed by iodine oxidation. Then DMT groups over the whole chip were removed by TCA chemistry, along with acetylated capping to stabilize unreacted aminoxyl group. LCMS results showed high efficiency of deblocking (greater than 97%) and coupling (greater than 90%) of different regular amidites; meanwhile non-active area almost showed no signal of deblocking product (FIG. 4).Attorney Docket No. 00415-0062-00304Example 2 - DNA Synthesis Using Quinone Oxime as a Protecting Group

[0193] A 5’-oxime dT phosphoramidite was obtained to first demonstrate the deprotection and coupling in a chemical pathway. A 11-mer 5 ’-oxime protected poly-deoxythymdine (dT) was prepared via a oligonucleotide synthetic cycle using solid-phase based flow cell method. A reducing reagent (e.g., DTT) was then introduced and incubated for a certain time to remove the oxime moiety, followed by coupling with another layer of deoxyadenosine (dA). Meanwhile, an identical parallel run of 11-mer dT is also provided as a control experiment but without the reducing reagent injection. The reduced run reported aN+1 efficiency while the control run hardly shows any +dA product (e.g.. FIG. 8), indicating oxime group was a stable moiety in phosphoramidite chemistry.

[0194] An electrochemically deblock protocol was also evaluated, first by evaluating various e- deblock solutions. Methylene blue was used as an auxiliary7agent to help transport electrons between cathodes and DNA molecules in aqueous solution (e.g., FIGs. 9A-9B). A water solution including 10 mM methylene blue (MB), 50 mM tetraethylammonium p- toluenesulfonate (TEA-PTS) and 0.5 mM acetic acid was prepared as the e-deblock solution. The pH of the solution prior to addition of acid was 5.37 at 20. 1 degrees Celsius, while the pH was 3.44 after addition of the acid at 18.7 degrees Celsius. A similar deblock assay was used in e-deblock study as well. 5’-oxime 11-mer dT was first synthesized on an entire microelectrode array. Then a variety of potential was applied to different areas of the chip with a single pulse of 80 seconds, which was followed by washing and dA coupling. The oligos were respectively collected and inspected with LCMS. Results are provided in Table 2 and LCMS data is provided in FIGs. 10A-10B. T11 refers to the failed deblocking and coupling results, while T11-A refers to the successful deblocking and coupling results. 87% of T11-A was achieved under -1.9V. and the deblocking efficiency failed to increase when reductive potential went lower than -1.9V. Meanwhile, around 16% of oxime was removed in 0V devices where no current was injected.Table 2Attorney Docket No. 00415-0062-00304

[0195] In order to observe the spatiosel activity of an oxime e-deblocking process, a fluorescence assay was performed to demonstrate the potency of localizing deblocking within the active microelectrodes’ region, thus to further grow different DNA on the same chip. 5 ’-oxime dTl 1 was prepared and MB cathodic reductive deblock was triggered on every other microelectrode. Next, a layer of tetramethylrhodaminyl amidite (Tamra-dT) was introduced to label all the deblocked region with fluorophore. Microscope images showed the oxime deblocking was well confined within the active area in both lum (FIG. 11A) and 2 urn (FIG. 11B) pitch apart.

[0196] The methylene blue based e-deblock protocol was used to prepare 9-mer poly dT with the aid of a DNA automated synthetic machine. Further details of the subroutine are provided in FIG. 12. According to its mass spectroscopy results, the major product dT9 peak appears at 2.74 min shown in FIGs. 13A-13B. This indicated longer DNA chain synthesis could be achieved with this aqueous MB cathodic process.Example 3 - DNA Synthesis Using Benzoquinone Oxime

[0197] A benzoquinone-derived oxime was generated by combining a 3 '-aminooxy (-ONH2)- protected nucleotide with benzoquinone. Without wishing to be bound by any theory, because aminooxy -modified nucleotides are useful in enzymatic synthesis, such nucleotides could serve as an alternative process for such type of e-chem synthesis as demonstrated herein. An in-situ condensation of a S'-ONFL-terminated oligonucleotide with benzoquinone, followed by electrochemical cleavage of the oxime, was performed according to the scheme presented in FIG. 16. A 3'-ONH2-protected poly(dT) 12-mer seed oligonucleotide was synthesized on a solid support on top of a passive array. The support was treated with benzoquinone to convert the 3'- ONH2 functionality to a 3 '-benzoquinone oxime, which was subsequently deprotected by cathodic reduction in the presence of methylene blue at -1.9 V. Thereafter, 3'-ONH2- deoxyadenosine-5 '-triphosphate (3'-ONH2-dATP) was enzymatically incorporated to extend the oxime deprotected strands. The sequential oxime formation, electrochemical deblocking, and enzymatic extension afforded altogether an overall conversion rate of 55%, summarized below in Table 3.Attorney Docket No. 00415-0062-00304Table 3

[0198] While preferred embodiments of the present subject matter have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the present subject matter. It should be understood that various alternatives to the embodiments of the present subject matter described herein may be employed in practicing the present subject matter.

[0199] The present disclosure is further described by the following non-limiting items.

[0200] Item 1. A composition for polynucleotide synthesis comprising:(a) a nucleoside; and(b) at least one protecting group, wherein the protecting group is configured for electrochemical removal under mild conditions.

[0201] Item 2. The composition of item 1, wherein mild conditions comprises use of aqueous solvents.

[0202] Item 3. The composition of item 1, wherein mild conditions comprises use of less acid for deprotection than DMT.

[0203] Item 4. The composition of item 1, wherein the at least one protecting group is a 5’ protecting group on the nucleoside.

[0204] Item 5. The composition of item 1, wherein the at least one protecting group is a 3’ protecting group on the nucleoside.

[0205] Item 6. The composition of item 1. wherein the composition comprises two protecting groups.

[0206] Item 7. The composition of item 1, wherein the at least one protecting group comprises an acid-cleavable protecting group.

[0207] Item 8. The composition of item 1. wherein the at least one protecting group comprises a base-cleavable protecting group.

[0208] Item 9. The composition of item 1, wherein the at least one protecting group is connected to a 5’ oxygen of the nucleoside by a nitrogen atom.

[0209] Item 10. The composition of item 1, wherein the composition comprises the structure:Attorney Docket No. 00415-0062-00304wherein B is an optionally protected nucleobase;R1and R2are independently selected at each occurrence from hydrogen, halogen, Ci-io alkyl, C 1-10 heteroalkyl, -SR4, -N(R4)2, -N+(R5)3, -C(O)R4, -C(O)OR4, -C(O)N(R4)2, - N(R4)C(O)R4, -N(R4)C(O)OR4, -N(R4)C(O)N(R4)2, -N(R4)C(S)N(R4)2, -N(R4)S(O)2(R4), -S(O)R4, -S(O)2R4. -S(O)2N(R4)2, -NO2, =S. -N=(R7), -CN, -P(O)(OR6)2, -P(O)R6(OR6), -P(OR6)N(R6)2, -S(O)2OR4, C3-10 carbocycle and 3- to 10-membered heterocycle, wherein the C1-10 alkyl, C 1-10 heteroalkyl, C3-10 carbocycle, or 3- to 10- membered heterocycle is optionally substituted with one or more substituents independently selected from halogen, -OR4, -SR4, -N(R4)2, -N+(R5)3, -C(O)OR4, - P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, -S(O)2R4. and =0;R3is selected from hydrogen, halogen, hydroxyl, C1-10 alkyl, C 1-10 heteroalkyl, -SR4, - N(R4)2, -N+(R5)3, -C(O)R4, -C(O)OR4, -OC(O)R4, -OC(O)N(R4)2, -C(O)N(R4)2, - N(R4)C(O)R4, -N(R4)C(O)OR4, -N(R4)C(O)N(R4)2, -N(R4)C(S)N(R4)2, -N(R4)S(O)2(R4), -S(O)R4, -S(O)2R4. -S(O)2N(R4)2, -N02. =S. -N=(R7). -CN, -P(O)(OR6)2, -P(O)R6(OR6), -P(OR6)N(R6)2, -S(O)2OR4, C3-10 carbocycle and 3- to 10-membered heterocycle, wherein the C1-10 alkyl, C 1-10 heteroalkyl, C3-10 carbocycle, or 3- to 10- membered heterocycle is optionally substituted with one or more substituents independently selected from halogen, -OR4, -SR4, -N(R4)2, -N+(R5)3, -C(0)0R4, - P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, -S(O)2R4, and =0;R4is independently selected at each occurrence from hydrogen, C1-10 alkyl, and C1-10 heteroalkyl, wherein the C1-10 alkyl or C1-10 heteroalkyl is optionally substituted with one or more substituents independently selected from: halogen. -OR8, -SR8, -N(R8)2. - N+(R5)3, -C(0)0R8, -P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, -S(O)2R8, =0, and C3-10 carbocycle, wherein each C3-10 carbocycle is optionally substituted with one or more substituents independently selected from halogen, -OR8. C1-6 alkyl, C1-6 haloalkyl, C1-6 hydroxyalkyl, and =0;R5is independently selected at each occurrence from hydrogen and C1-4 alkyl;R6is independently selected at each occurrence from hydrogen, C1-6 alkyl, and -CN;Attorney Docket No. 00415-0062-00304R7is selected from C3-10 carbocycle and 3- to 10-membered heterocycle, wherein each C3-10 carbocycle and 3- to 10-membered heterocycle is optionally substituted with one or more substituents independently selected from -OH, C1-6 alkyl, C1-6 haloalkyl, C1-6 hydroxyalkyl, and =0; andR8is selected from hydrogen and Ci-4 alkyl.

[0210] Item 11. The composition of item 10, wherein R1or R2is -N(R4)2, -N(R7), - P(OR6)N(R6)2, or C1-10 alkyl.

[0211] Item 12. The composition of item 10 or 11, wherein R^omprise a mono, di, tri or polyphosphate.

[0212] Item 13. The composition of any one of items 10-12, wherein R4is independently selected at each occurrence from hydrogen and C1-10 alkyl.

[0213] Item 14. The composition of item 13, wherein the C1-10 alkyl is substituted with one or more substituents, wherein the one or more substituents is a C3-10 carbocycle.

[0214] Item 15. The composition of item 14, wherein the C3-10 carbocycle substituted with -OR8.

[0215] Item 16. The composition of any one of items 10-15, wherein R8is a C1-4 alkyl.

[0216] Item 17. The composition of any one of items 10-16, wherein R1or R2has the structure:

[0217] Item 18. The composition of any one of items 10-17, wherein R7is a C3-10 carbocycle.

[0218] Item 19. The composition of item 18, wherein the C3-10 carbocycle is substituted with =0.

[0219] Item 20. The composition of any one of items 10-19, wherein R1or R2has the structure:

[0220] Item 21. The composition of any one of items 10-20, wherein R6is independently selected at each occurrence from Ci-e alkyl and -CN.

[0221] Item 22. The composition of any one of items 10-21, wherein R1or R2has the structure:Attorney Docket No. 00415-0062-00304

[0222] Item 23. The composition of any one of items 10-22, wherein the Ci-io alkyl is substituted with -OR4.

[0223] Item 24. The composition of item 23, wherein R4is a C 1-10 alkyl.

[0224] Item 25. The composition of any one of items 10-24, wherein R1or R2has the structure:

[0225] Item 26. The composition of item 10, wherein the composition comprises the structure:Attorney Docket No. 00415-0062-00304

[0226] Item 27. The composition of item 10, wherein the composition comprises the structure:Attorney Docket No. 00415-0062-00304or polyphosphate.

[0227] Item 28. The composition of item 10, wherein the composition comprises the structure:

[0228] Item 29. The composition of item 10, wherein the composition comprises the structure:Attorney Docket No. 00415-0062-00304

[0229] Item 30. The composition of item 10, wherein when R1is hydrogen, R2is not hydrogen.

[0230] Item 31. The composition of item 10, wherein when R2is hydrogen, R1is not hydrogen.

[0231] Item 32. A polynucleotide comprising the composition of any one of items 1-31.

[0232] Item 33. The polynucleotide of item 32, wherein the composition is attached to the 5‘ terminus of the polynucleotide.

[0233] Item 34. The polynucleotide of item 32, wherein the composition is attached to the 3’ terminus of the polynucleotide.

[0234] Item 35. A method for polynucleotide synthesis comprising extending a polynucleotide, wherein the polynucleotide is extended by:(a) deprotecting a first protected nucleotide to generate a deprotected nucleotide; wherein the first protected nucleotide comprises the composition of any one of items 1-34.

[0235] Item 36. The method of item 35, wherein the method further comprises:(b) contacting the deprotected nucleotide with a second protected nucleotide thereby extending the polynucleotide; and(c) repeating (a)-(b) to synthesize the polynucleotide.

[0236] Item 37. The method of item 36. wherein the second protected nucleotide comprises the composition of any one of items 1 -34.

[0237] Item 38. The method of any one of items 35-37, wherein the deprotecting comprises exposing the first protected nucleotide or the second protected nucleotide to a solvent.

[0238] Item 39. The method of any one of items 35-38, wherein deprotecting the first protected nucleotide or the second protected nucleotide comprises applying a voltage.Attorney Docket No. 00415-0062-00304

[0239] Item 40. The method of item 39. wherein applying the voltage comprises reductive deblocking.

[0240] Item 41. The method of item 40, wherein the voltage is about -1 V to about -2 V.

[0241] Item 42. The method of item 40, wherein the voltage is about -1.3V to about -1.9V.

[0242] Item 43. The method of any one of items 35-42. wherein the deprotection comprises a deprotection efficiency of at least 85%.

[0243] Item 44. The method of item 39, wherein applying the voltage comprises generating acid.

[0244] Item 45. The method of item 39, wherein the acid is generated by the solvent in fluid communication with the first protected nucleotide.

[0245] Item 46. The method of item 39, wherein the voltage is applied for about 50 seconds.

[0246] Item 47. The method of any one of items 35-46, wherein the deprotection comprises a deprotection efficiency of at least 87%.

[0247] Item 48. The method of any one of items 35-46, wherein the deprotection comprises a deprotection efficiency of at least 95%.

[0248] Item 49. The method of any one of items 35-46, w herein the deprotection comprises a deprotection efficiency of at least 97%.

[0249] Item 50. The method of any one of items 35-46, wherein the deprotection comprises a deprotection efficiency of at least 99%.

[0250] Item 51. The method of any one of items 36-50, w herein contacting comprises coupling the second protected nucleotide to the deprotected nucleotide.

[0251] Item 52. The method of any one of items 36-51, wherein the second protected nucleotide and the deprotected nucleotide are coupled via phosphoramidite synthesis or enzymatic synthesis.

[0252] Item 53. The method of any one of items 35-52, w herein the polynucleotide is attached to a solid support.

[0253] Item 54. The method of item 53, wherein the first protected nucleotide is attached to the solid support.

[0254] Item 55. The method of item 53 or 54, wherein the solid support comprises an addressable surface.

[0255] Item 56. The method of any one of items 53-55, wherein the solid support comprises a CMOS chip.

[0256] Item 57. The method of any one of items 53-56, w herein the solid support comprises one or more active areas for polynucleotide synthesis.

[0257] Item 58. The method of item 57, wherein the one or more active areas have a pitchAttorney Docket No. 00415-0062-00304 distances of about 1 um.

[0258] Item 59. The method of item 57, wherein the one or more active areas have a pitch distances of about 2 um.

Claims

Attorney Docket No. 00415-0062-00304CLAIMSWhat is claimed is:

1. A composition for polynucleotide synthesis comprising: a nucleoside; and a protecting group configured for electrochemical removal under mild conditions.

2. The composition of claim 1, wherein the composition comprises the structure:wherein B is a protected nucleobase;R1and R2are independently selected at each occurrence from hydrogen, halogen, Ci-io alkyl, C i-io heteroalkyl, -SR4, -N(R4)2, -N+(R5)3, -C(O)R4, -C(O)OR4, -C(O)N(R4)2, - N(R4)C(O)R4, -N(R4)C(O)OR4, -N(R4)C(O)N(R4)2, -N(R4)C(S)N(R4)2, -N(R4)S(O)2(R4), -S(O)R4, -S(O)2R4, -S(O)2N(R4)2, -NO2, =S, -N=(R7), -CN, -P(O)(OR6)2, -P(O)R6(OR6), -P(OR6)N(R6)2, -S(O)2OR4, C3-10 carbocycle and 3- to 10-membered heterocycle. wherein the C1-10 alkyl, C1-10 heteroalkyl, C3-10 carbocycle, or 3- to 10- membered heterocycle is optionally substituted with one or more substituents independently selected from halogen, -OR4, -SR4, -N(R4)2, -N+(R5)3, -C(O)OR4, - P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, -S(O)2R4, and =0;R3is selected from hydrogen, halogen, hydroxyl, C1-10 alkyl, C 1-10 heteroalkyl, -SR4, - N(R4)2, -N+(R5)3, -C(O)R4, -C(O)OR4, -OC(O)R4, -OC(O)N(R4)2, -C(O)N(R4)2, - N(R4)C(O)R4, -N(R4)C(O)OR4, -N(R4)C(O)N(R4)2, -N(R4)C(S)N(R4)2, -N(R4)S(O)2(R4), -S(O)R4, -S(O)2R4, -S(O)2N(R4)2, -NO2, =S, -N=(R7), -CN, -P(O)(OR6)2, -P(O)R6(OR6), -P(OR6)N(R6)2, -S(O)2OR4, C3-10 carbocycle and 3- to 10-membered heterocycle. wherein the C1-10 alkyl, C 1-10 heteroalkyl, C3-10 carbocycle, or 3- to 10- membered heterocycle is optionally substituted with one or more substituents independently selected from halogen, -OR4, -SR4, -N(R4)2, -N+(R5)3, -C(O)OR4, - P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, -S(O)2R4, and =0;R4is independently selected at each occurrence from hydrogen, C1-10 alkyl, and C1-10 heteroalkyl, wherein the C1-10 alkyl or C1-10 heteroalkyl is optionally substituted with one or more substituents independently selected from: halogen. -OR8, -SR8, -N(R8)2. -Attorney Docket No. 00415-0062-00304N+(R5)3, -C(O)OR8, -P(O)(OR6)2, -P(O)R6(OR6), -S(O)2OR6, -S(O)2R8. =0, and C3-10 carbocycle, wherein each C3-10 carbocycle is optionally substituted with one or more substituents independently selected from halogen, -OR8, C1-6 alkyl, C1-6 haloalkyl, Ci-ehydroxyalkyl, and =0;R5is independently selected at each occurrence from hydrogen and C1-4 alkyl;R6is independently selected at each occurrence from hydrogen, C1-6 alkyl, and -CN;R7is selected from C3-10 carbocycle and 3- to 10-membered heterocycle, wherein each C3-10 carbocycle and 3- to 10-membered heterocycle is optionally substituted with one or more substituents independently selected from -OH, C1-6 alkyl, C1-6 haloalkyl, C1-6 hydroxyalkyl, and =0; andR8is selected from hydrogen and C1-4 alkyl.

3. The composition of claim 1, wherein the composition comprises the structure:Attorney Docket No. 00415-0062-003044. The composition of claim 1, wherein the composition comprises the structure:Attorney Docket No. 00415-0062-003045. The composition of claim 1, wherein the composition comprises the structure:

6. The composition of claim 1, wherein the composition comprises the structure:Attorney Docket No. 00415-0062-003047. The composition of claim 2, wherein R1or R2comprises the structure:

8. A polynucleotide comprising the composition of any one of claims 1-7 attached to a 5’ terminus of the polynucleotide or attached to a 3’ terminus of the polynucleotide.

9. A method for polynucleotide synthesis, the method comprising deprotecting a first protected nucleotide to generate a deprotected nucleotide, wherein the first protected nucleotide comprises the composition of any one of claims 1-7.

10. The method of claim 9, wherein the method further comprises contacting the deprotected nucleotide with a second protected nucleotide, thereby extending a polynucleotide including the deprotected nucleotide.Attorney Docket No. 00415-0062-0030411. The method of claim 10, wherein the second protected nucleotide comprises the composition of any one of claims 1-7.

12. The method of any one of claims 9-11, wherein the deprotecting the first protected nucleotide comprises contacting the first protected nucleotide to a solvent.

13. The method of any one of claims 9-12, wherein deprotecting the first protected nucleotide comprises applying a voltage.

14. The method of claim 13, wherein the voltage is about -1 V to about -2 V.

15. The method of any one of claims 10-14, wherein the polynucleotide is attached to a solid support.

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