Tagmentation using immobilized transposomes with linkers

Abstract

Providing tagmentation using immobilized transposomes with linkers. The present disclosure relates to methods, compositions, and kits for processing target nucleic acids, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes bound to a solid support. The present disclosure provides transposome complexes comprising a transposase, a first transposon, and a second transposon, wherein the first transposon comprises (a) a 3' portion comprising a first transposon end sequence and (b) a first adapter sequence at the 5' end of the first transposon end sequence, and the second transposon may comprise a second transposon end sequence complementary to at least a portion of the first transposon end sequence.

Description

[Technical field]

[0001] INCORPORATION BY REFERENCE TO ANY PRIORITY APPLICATION This application claims the benefit of priority to U.S. Provisional Patent Application No. 62 / 461,620, filed February 21, 2017, which is hereby incorporated by reference in its entirety.

[0002] Reference to sequence listing This disclosure includes a sequence listing in electronic format, which is provided as a file entitled ILLINC-398WO_Sequence_Listing.txt, approximately 7KB in size, created on February 20, 2017. The information in the electronic format of this sequence listing is incorporated herein by reference in its entirety.

[0003] background Field The present disclosure relates to methods, compositions, and kits for processing nucleic acids, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on a solid support. [Background technology]

[0004] Current protocols for next-generation sequencing (NGS) of nucleic acid samples routinely use a sample preparation process that converts DNA or RNA into a library of fragmented, sequenceable templates. Sample preparation methods often require multiple steps and material transfers, as well as expensive equipment to effect fragmentation, and are therefore often difficult, tedious, lengthy, expensive, and inefficient.

[0005] In one approach, a nucleic acid fragment library can be prepared using a transposome-based method in which two transposon end sequences (one linked to a tag sequence) and a transposase form a transposome complex. The transposome complex is used to fragment and tag the target nucleic acid in solution to generate a sequencer-ready tagmented library. The transposome complex can be immobilized on a solid surface (e.g., through biotin added at the 5' end of one of the two end sequences). The use of immobilized transposomes offers significant advantages over solution-phase approaches by reducing hands-on and overall library preparation time, cost, and reagent requirements, lowering sample input requirements, and allowing the use of unpurified or degraded samples as the starting point for library preparation. Exemplary transposition procedures and systems for immobilization of transposomes on solid surfaces that produce uniform fragment sizes and library yields are described in detail in WO2014 / 108810 and WO2016 / 189331, each of which is incorporated by reference herein in its entirety.

[0006] In some bead-based tagmentation methods described in PCT Publication No. WO2016 / 189331 and US 2014 / 093916A1, transposomes are bound to magnetic beads using biotin-streptavidin interaction.During the subsequent PCR amplification step of the protocol, biotin-streptavidin bond is broken by heat denaturation, thereby releasing biotinylated tagmentation product into solution.Amplicons with sequences of interest, or target amplicons, can be enriched by, for example, hybridization capture and sequenced if desired.

[0007] However, when libraries prepared by tagmentation using immobilized transposomes are enriched for certain regions of the genome using general hybridization capture methods, lower read enrichment for certain regions in the genome may be achieved compared to enrichment for libraries generated using, for example, a solution-based transposome approach.

[0008] Furthermore, the stability of the transposome complex bound to the support varies depending on the linker construct used to connect the transposome complex to the support. If the complex is removed from the support during storage or library preparation, the quality and efficiency of the resulting library will be affected. Therefore, there is a need for immobilized transposome complexes with improved stability and related methods that show improved efficiency of tagmentation library generation, and thus increased lead enrichment of the resulting library. There is also a need for compositions and methods that improve lead enrichment of the resulting library. The present disclosure relates to support-bound transposome complexes having modified linker and component arrangements. The present disclosure provides methods and compositions for generating sequence-ready nucleic acid libraries using such modified complexes. [Prior art documents] [Patent documents]

[0009] [Patent Document 1] International Publication No. 2014 / 108810 [Patent Document 2] International Publication No. 2016 / 189331 [Patent Document 3] US Patent Application Publication No. 2014 / 093916 Summary of the Invention [Means for solving the problem]

[0010] Abstract The present disclosure relates to methods, compositions, and kits for processing nucleic acids, including methods and compositions for fragmenting and tagging DNA using transposome complexes on solid supports.

[0011] The present disclosure provides a transposome complex comprising a transposase, a first transposon, and a second transposon, wherein the first transposon comprises (a) a 3' portion comprising a first transposon end sequence and (b) a first adaptor sequence at the 5' end of the first transposon end sequence, and the second transposon comprises a second transposon end sequence complementary to at least a portion of the first transposon end sequence. Typically, the first transposon end sequence and the second transposon end sequence anneal together to form a double-stranded transposon end sequence that is recognized by the transposase, and the combination forms a functional transposome complex.

[0012] In some aspects, the transposome complex comprises a cleavable linker that can connect the first transposon (and thus the complex) to the solid support. In such aspects, the first end of the cleavable linker is bound to the 5' end of the first adaptor sequence, and in some aspects, the second end of the cleavable linker is bound to an affinity element. The affinity element can be bound (covalently or non-covalently) to an affinity binding partner on the solid support. In some aspects, the affinity element is bound (covalently or non-covalently) to an affinity binding partner on the solid support to provide a transposome complex bound to a solid support. These complexes are 5'-linker transposome complex and 5'-linker transposome complex bound to a solid support.

[0013] In other aspects, the transposome complex includes a 3' linker that can connect the second transposon (and thus the complex) to the solid support. In such aspects, the first end of the linker is attached to the 3' end of the second transposon, and the second end of the linker is attached to an affinity element. The affinity element can be attached (covalently or non-covalently) to an affinity binding partner on the solid support. In some aspects, the affinity element is attached (covalently or non-covalently) to an affinity binding partner on the solid support to provide a transposome complex attached to a solid support. In some aspects, the linker is a cleavable linker. These complexes are 3'-linker transposome complexes and 3'-linker transposome complexes attached to a solid support.

[0014] In some aspects, the present disclosure relates to modified oligonucleotides.In some aspects, the modified oligonucleotides include a first transposon and a second transposon, wherein the first transposon comprises (a) a 3' portion comprising a first transposon end sequence and (b) a first adaptor sequence at the 5' end of the first transposon end sequence, and the second transposon comprises a second transposon end sequence that is complementary to and anneals to at least a portion of the first transposon end sequence, wherein the first end of a cleavable linker is bound to the 5' end of the first adaptor sequence, and in some aspects, the second end of the cleavable linker is bound to an affinity element.

[0015] In other aspects, the modified oligonucleotide comprises a first transposon and a second transposon, wherein the first transposon comprises (a) a 3' portion comprising a first transposon end sequence, and (b) a first adaptor sequence at a 5' end of the first transposon end sequence, the second transposon comprises a second transposon end sequence complementary to and annealed to at least a portion of the first end sequence, and wherein a first end of a linker is attached to the 3' end of the second transposon and a second end of the linker is attached to an affinity element. In some aspects, the linker is a cleavable linker.

[0016] In some embodiments of a 3'-linker transposome complex, the affinity element and linker have a structure of formula (I), (I'), (Ia), (Ib), (Ic), (I(a)), (I(b)), or (I(c)) as described herein. In some aspects, the affinity element is covalently linked to the 3' end of the second transposon, wherein the affinity element and linker have the structure of formula (I): [ka] where: AE is an affinity element; Y is C 2-6 is alkylene; X 1 , O, NR 1 , or S; Here, R 1 is H or C 1-10 is alkyl; n is an integer selected from the group consisting of 1, 2, 3, 4, 5, and 6; X 2 is O, CH2, or S; R a is H or -OH; and Z is R ais H, or R a is H or OH; where [ka] is a mark of the connection point to the second transposon.

[0017] In some aspects, the linkers described herein are 5' linkers, where the phosphate group in formula (I) is a terminal phosphate group at the 5' position of the terminal nucleotide of the first transposon. In some aspects, the linkers described herein are 3' linkers, where the phosphate group in formula (I) is connected to the 3' hydroxyl of the second transposon oligonucleotide (e.g., the 3' terminal nucleotide).

[0018] In other aspects, the present disclosure provides a method for generating a library of tagged nucleic acid fragments from a double-stranded target nucleic acid, comprising incubating the target with a transposome complex bound to a solid support as described herein.In some aspects, the method comprises treating the target with the immobilized transposome complex under conditions in which the target is fragmented and the 3' end of the first transposon is tethered to the 5' end of the target fragment to generate a plurality of 5' tagged target fragments.In some embodiments, a plurality of transposome complexes are used.

[0019] In some embodiments, the method further comprises amplifying one or more of the 5' tagged target fragments. In some embodiments, the method further comprises sequencing one or more of the 5' tagged target fragments or their amplification products.

[0020] Accordingly, some further embodiments of the present disclosure relate to a method for generating a library of tagged nucleic acid fragments, the method comprising: providing a solid support comprising a transposome complex as described herein immobilized on said solid support; and contacting the solid support with a double-stranded target nucleic acid under conditions sufficient to fragment the target nucleic acid into a plurality of target fragments and to ligate the 3' end of the first transposon to the 5' end of the target fragments to provide a plurality of 5'-tagged target fragments; Includes:

[0021] In some aspects, the method further comprises amplifying the 5' tagged target fragment.

[0022] In some aspects, the disclosure provides libraries of 5'-tagged target fragments generated by the methods described herein.

[0023] The present disclosure further provides a method for preparing modified oligonucleotides, transposome complexes, and transposome complexes bound to solid support as described herein.In some aspects, such methods include treating transposase with a first and a second transposon as described herein under suitable conditions to form the complex.The method for preparing transposome complexes bound to solid support includes incubating a transposome complex as described herein with a solid support that contains an affinity binding partner under sufficient conditions for the affinity element to bind (covalently or non-covalently) to the affinity binding partner.

[0024] In some embodiments of the compositions and methods described herein, the transposome complexes comprise two populations, where the first adapter sequences in each population are different. [Brief description of the drawings]

[0025] [Figure 1] FIG. 1 illustrates exemplary steps of a method for attaching one embodiment of a transposome complex to a bead surface.

[0026] [Diagram 2] FIG. 2 illustrates a schematic of an exemplary tagmentation process on a bead surface through cluster formation on a flow cell.

[0027] [Diagram 3] FIG. 3 shows exemplary steps of a method for using transposome complexes immobilized on a bead surface to fragment and tag DNA, followed by target enrichment that results in contaminating off-target reads.

[0028] [Figure 4] FIG. 4 shows exemplary steps of a method for fragmenting and tagging DNA followed by target enrichment using transposome complexes immobilized on a bead surface using an enzyme-cleavable linker.

[0029] [Figure 5A] FIG. 5A shows an example of a biotinylated 5′ end of a transposon sequence attached to a solid surface for tagmentation and subsequent amplification.

[0030] [Figure 5B] FIG. 5B shows an example of a biotinylated 3′ end of a transposon sequence attached to a solid surface for tagmentation and subsequent amplification.

[0031] [Figure 6A] FIG. 6A compares library yields from streptavidin bead-based solid-phase tagmentation using transposome complexes with two different 3′-biotinylated linkers.

[0032] [Figure 6B] FIG. 6B shows accelerated stability data for a sample library prepared from streptavidin bead-based solid-phase tagmentation using a transposome complex having a 3'-biotinylated linker of formula (I(a)) after 4 months of aging, compared to a sample library prepared from a non-aged batch (control) of the same complex.

[0033] [Figure 6C] Figure 6C shows accelerated stability data for sample libraries prepared from transposome complexes with a 3'-biotinylated linker of formula (I(c)) after 4 and 8 months of time-effects, compared to a sample library prepared from a non-time-effected complex (control).

[0034] [Figure 7A] FIG. 7A shows the target insert size of DNA molecules as a function of complex density using streptavidin bead-based solid-phase library preparation, where the beads contain transposome complexes immobilized to the beads through 3′-biotinylated linkers.

[0035] [Figure 7B] FIG. 7B is a line graph showing target insert size of DNA molecules as a function of SPRI conditions using streptavidin beads with immobilized transposome complexes containing hyperactive Tn5 transposase and 3′-biotinylated linkers, and a complex density of 100 nM.

[0036] [Figure 7C] FIG. 7C is a line graph showing target insert size of DNA molecules as a function of SPRI conditions using streptavidin beads with immobilized transposome complexes containing hyperactive Tn5 transposase and 3′-biotinylated linkers, and a complex density of 600 nM. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0037] Detailed Description Libraries of fragmented nucleic acids are often made from genomic nucleic acids for use in next-generation sequencing (NGS) applications. The present disclosure provides methods, compositions, and kits for immobilized transfer library preparation. The immobilized transfer library preparation method is rapid compared to other library preparation methods and is effective in preparing libraries from both gross or non-purified samples (e.g., blood, sputum, cell extracts, etc.) and purified samples (e.g., purified genomic nucleic acids). In general, transposomes are immobilized on a substrate (e.g., slides or beads) using covalent or non-covalent binding partners (e.g., affinity elements and affinity binding partners) (Figure 1). For example, transposome complexes are immobilized on the streptavidin-coated beads through biotinylated linkers bound to the transposome complexes. The target nucleic acid is captured by the immobilized transposome complexes, and the nucleic acid is fragmented and tagged ("tagmentation"). The tagged fragments are amplified, the amplicons of interest are optionally captured (eg, via hybridization probes), and the tagged fragments are sequenced.

[0038] The use of solid support-linked transposome complexes for library preparation reduces the need for normalization of sample input going into the library preparation process and normalization of library output before enrichment or sequencing steps. Using these complexes also produces libraries with more consistent insert sizes compared to solution-phase methods, even when various sample input concentrations are used. However, certain transposome complexes with biotinylated linkers have been observed to have reduced stability. Furthermore, the construction of certain support-bound complexes produces off-target products; in particular, hybridization and capture of amplicons of 5'-tagged target fragments can be contaminated by fragments of nucleic acid that are still hybridized to the immobilized nucleic acid (Figure 3). This inefficiency can result in waste of reagents, as well as sequencing instruments or flow cells with off-target fragments and sequencing data. The present application discloses various transposome complex designs that address the issue of library quality and reduce off-target capture, as well as complexes with modified linkers that exhibit improved chemical stability.

[0039] In some embodiments, the nucleic acid library obtained by the methods disclosed herein can be sequenced using any suitable nucleic acid sequencing platform to determine the nucleic acid sequence of the target sequence. In some respects, the sequence of interest correlates or is associated with one or more congenital or genetic disorders, pathogenicity, antibiotic resistance, or genetic modification. Sequencing can be used to determine the nucleic acid sequence of short tandem repeats, single nucleotide polymorphisms, genes, exons, coding regions, exomes, or portions thereof. Thus, the methods and compositions described herein relate to making sequenceable libraries that are useful, but not limited to, in cancer and disease diagnosis, prognosis, and therapeutics, DNA fingerprinting applications (e.g., DNA data banking, criminal casework), metagenomic research and drug discovery, agrigenomic applications, and pathogen identification and monitoring.

[0040] The number of steps required to convert a target nucleic acid (e.g., DNA) into an adaptor-modified template ready for next-generation sequencing can be minimized by using transposase-mediated fragmentation and tagging. This process is referred to herein as "tagmentation" and involves the modification of the target nucleic acid by a transposome complex that includes a transposase enzyme complexed with a transposon pair that includes a single-stranded adaptor sequence and a double-stranded transposon end sequence region, often with optional additional sequences designed for a specific purpose. Tagmentation results in simultaneous fragmentation of the target nucleic acid and ligation of adaptors to the 5'-ends of both strands of the double-stranded nucleic acid fragment. If the transposome complex is bound to a support, the resulting fragments are bound to a solid support (either directly in the case of a 5'-linked transposome complex, or via hybridization in the case of a 3'-linked transposome complex) after the tagmentation reaction.

[0041] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art. All patents, applications, published applications and other publications referred to herein are incorporated by reference in their entirety unless otherwise stated. In the event that there are multiple definitions for terms herein, the terms in this section shall prevail unless otherwise stated. As used in this specification and the appended claims, the singular forms "a," "an," and "the" include plural references unless the context clearly dictates otherwise. Conventional methods of mass spectrometry, NMR, HPLC, proton chemistry, biochemistry, recombinant DNA technology and pharmacology are used unless otherwise indicated. The use of "or" or "and" means "and / or" unless otherwise stated. Additionally, the use of the term "including" and other forms (e.g., "include", "includes", and "included") is not limiting. As used herein, whether in a transitional phrase or in the body of a claim, the terms "comprise(s)" and "comprising" should be construed to have an open-ended meaning. That is, these terms should be construed synonymously with the words "having at least" or "including at least". When used in the context of a process, the term "comprising" means that the process includes at least the recited steps, but may include additional steps. When used in the context of a compound, composition, or device, the term "comprising" means that the compound, composition, or device includes at least the recited features or components, but may also include additional features or components.

[0042] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

[0043] chemical terms As used herein, "alkyl" refers to a straight or branched hydrocarbon chain that is fully saturated (i.e., contains no double or triple bonds). The alkyl group may have 1 to 20 carbon atoms (wherever it appears herein, numerical ranges (e.g., "1 to 20" refer to each integer in the given range; e.g., "1 to 20 carbon atoms" means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 20 carbon atoms, but this definition also encompasses the occurrence of the term "alkyl" without a numerical range specified). The alkyl group may also be a medium size alkyl having 1 to 9 carbon atoms. The alkyl group may also be a lower alkyl having 1 to 6 carbon atoms. The alkyl group may also be a "C 1-4 By way of example only, "C alkyl" or a similar designation may be used. 1-6 "Alkyl" means that there are 1 to 6 carbon atoms in the alkyl chain, i.e., the alkyl chain is selected from the group consisting of methyl, ethyl, propyl, isopropyl, n-butyl, isobutyl, sec-butyl, and t-butyl. Representative alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, hexyl, and the like.

[0044] As used herein, "alkoxy" refers to a group of the formula -OR, where R is alkyl as defined above (e.g., C 1-9 Alkoxy refers to alkoxy groups including, but not limited to, methoxy, ethoxy, n-propoxy, 1-methylethoxy (isopropoxy), n-butoxy, isobutoxy, sec-butoxy, and tert-butoxy.

[0045] As used herein, "aryl" refers to an aromatic ring or ring system that contains only carbon in the ring backbone (i.e., two or more fused rings that share two adjacent carbon atoms). When aryl is a ring system, all rings in the system are aromatic. Aryl groups can have from 6 to 18 carbon atoms, although this definition also covers occurrences of the term "aryl" where no numerical range is specified. In some embodiments, aryl groups have from 6 to 10 carbon atoms. An aryl group is defined as "C 6-10 Aryl, C6 to C 10 Examples of aryl groups include, but are not limited to, phenyl, naphthyl, azulenyl, and anthracenyl.

[0046] An "aralkyl" or "arylalkyl" is an aryl group connected, as a substituent, through an alkylene group (e.g., "C 7-14 arylalkyl), benzyl, 2-phenylethyl, 3-phenylpropyl, and naphthylalkyl. In some cases, the alkylene group can be a lower alkylene group (i.e., 1-6 alkylene group).

[0047] As used herein, "carbocyclyl" refers to a non-aromatic ring or ring system that contains only carbon atoms in the backbone of the ring system. When a carbocyclyl is a ring system, two or more rings can be connected together in a fused, bridged, or spiro-connected fashion. A carbocyclyl can have any degree of saturation, provided that at least one ring in the ring system is not aromatic. Thus, carbocyclyl includes cycloalkyl, cycloalkenyl, and cycloalkynyl. A carbocyclyl group can have 3 to 20 carbon atoms, although this definition also encompasses the existence of the term "carbocyclyl" where no numerical range is specified. A carbocyclyl group can also be a medium sized carbocyclyl having 3 to 10 carbon atoms. A carbocyclyl group can also be a carbocyclyl having 3 to 6 carbon atoms. A carbocyclyl group is defined as a "C 3-6 Carbocyclyl may be designated as "carbocyclyl" or a similar designation. Examples of carbocyclyl rings include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclohexenyl, 2,3-dihydro-indene, bicycle[2.2.2]octanyl, adamantyl, and spiro[4.4]nonanyl.

[0048] As used herein, "C a ~C b (C a to C b )" or "C a-b " where "a" and "b" are integers refers to the number of carbon atoms in the specified group; that is, the group can contain from "a" to "b" carbon atoms (inclusive). Thus, for example, "C1-C4 alkyl" or "C 1-4 An "alkyl" group refers to all alkyl groups having 1 to 4 carbons, i.e., CH3-, CH3CH2-, CH3CH2CH2-, (CH3)2CH-, CH3CH2CH2CH2-, CH3CH2CH(CH3)-, and (CH3)3C-.

[0049] As used herein, the term "covalently attached" or "covalently bonded" refers to the formation of a chemical bond characterized by the sharing of electron pairs between atoms. For example, a covalently attached polymer coating refers to a polymer coating that forms a chemical bond with the functionalized surface of a substrate, as compared to bonding to the surface through other means, such as adhesion or electrostatic interactions. It is recognized that the polymer that is covalently attached to the surface can also be attached, for example, by physical adsorption, in addition to the covalent bond.

[0050] The term "halogen" or "halo" as used herein means any one of the radioactive stable atoms of Group 7 of the Periodic Table of the Elements, e.g., fluorine, chlorine, bromine, or iodine, with fluorine and chlorine being preferred.

[0051] As used herein, "heteroaryl" refers to an aromatic ring or ring system (i.e., two or more fused rings sharing two adjacent atoms) that contains one or more heteroatoms (i.e., elements other than carbon, including, but not limited to, nitrogen, oxygen, and sulfur) in the ring backbone. When a heteroaryl is a ring system, all rings in the system are aromatic. Heteroaryl groups can have 5 to 18 ring members (i.e., the number of atoms that make up the ring backbone, including carbon atoms and heteroatoms), although this definition also covers the occurrence of the term "heteroaryl" where no numerical range is specified. In some embodiments, heteroaryl groups have 5 to 10 ring members or 5 to 7 ring members. Heteroaryl groups may be designated as "5-7 membered heteroaryl," "5-10 membered heteroaryl," or similar designations. Examples of heteroaryl rings include, but are not limited to, furyl, thienyl, phthalazinyl, pyrrolyl, oxazolyl, thiazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, triazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, quinolinyl, isoquinlinyl, benzimidazolyl, benzoxazolyl, benzothiazolyl, indolyl, isoindolyl, and benzothienyl.

[0052] As used herein, "heterocyclyl" refers to a non-aromatic cyclic ring or ring system that contains at least one heteroatom in the ring backbone. Heterocyclyls may be joined together in a fused, bridged, or spiro-connected fashion. Heterocyclyls may have any degree of saturation, provided that at least one ring in the ring system is not aromatic. The heteroatoms may be present in either non-aromatic or aromatic rings in the ring system. Heterocyclyl groups may have 3-20 ring members (i.e., the number of atoms that make up the ring backbone, including carbon atoms and heteroatoms), although this definition also encompasses the existence of the term "heterocyclyl" where no numerical range is specified. Heterocyclyl groups may also be medium-sized heterocyclyls having 3-10 ring members. Heterocyclyl groups may also be heterocyclyls having 3-6 ring members. Heterocyclyl groups may be designated as "3-6 membered heterocyclyl" or similar designations. In preferred 6-membered monocyclic heterocyclyls, the heteroatoms are selected from 1 to 3 of O, N or S, and in preferred 5-membered monocyclic heterocyclyls, the heteroatoms are selected from 1 or 2 heteroatoms selected from O, N or S.Examples of heterocyclyl rings include azepinyl, acridinyl, carbazolyl, cinnolinyl, dioxolanyl, imidazolinyl, imidazolidinyl, morpholinyl, oxiranyl, oxepanyl, thiepanyl, piperidinyl, piperazinyl, dioxopiperazinyl, pyrrolidinyl, pyrrolidonyl, pyrrolidinyl, 4-piperidonyl, pyrazolinyl, pyrazolidinyl, 1,3-dioxinyl, 1,3-dioxanyl, 1,4-dioxinyl, 1,4-dioxanyl, 1,3-oxathiinyl, 1,4-oxathiinyl, 2H-1,2-oxazinyl, triaryl, ... Examples of aryl groups include, but are not limited to, oxanyl, hexahydro-1,3,5-triazinyl, 1,3-dioxolyl, 1,3-dioxolanyl, 1,3-dithiolyl, 1,3-dithiolanyl, isoxazolyl, isoxazolidinyl, oxazolinyl, oxazolidinyl, oxazolidinonyl, thiazolinyl, thiazolidinyl, 1,3-oxathiolanyl, indolinyl, isoindolinyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydro-1,4-thiazinyl, thiamorpholinyl, dihydrobenzofuranyl, benzimidazolidinyl, and tetrahydroquinoline.

[0053] As used herein, a substituted group is derived from an unsubstituted parent group in which one or more hydrogen atoms have been replaced with another atom or group. Unless otherwise indicated, when a group is considered to be "substituted", it is understood that the group can be any of C1-C6 alkyl, C1-C6 alkenyl, C1-C6 alkynyl, C1-C6 heteroalkyl, C3-C7 carbocyclyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), C3-C7-carbocyclyl-C1-C6-alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkoxy, C3-C7-carbocylyl-C1-C6-alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkoxy, C3-C7-carbocylyl-C1-C6-alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkoxy, C3-C7-carbocylyl-C1-C6-alkyl, C1-C6 ... aryl, and C1-C6 haloalkoxy), 3-10 membered heterocyclyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 3-10 membered heterocyclyl-C1-C6-alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), aryl (halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), -C6 haloalkyl, and C1-C6 haloalkoxy), aryl(C1-C6)alkyl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 5-10 membered heteroaryl (optionally substituted with halo, C1-C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), 5-10 membered heteroaryl(C1-C6)alkyl (halo, C1- optionally substituted with C6 alkyl, C1-C6 alkoxy, C1-C6 haloalkyl, and C1-C6 haloalkoxy), halo, cyano, hydroxy, C1-C6 alkoxy, C1-C6 alkoxy(C1-C6)alkyl (i.e., ether), aryloxy, sulfhydryl (mercapto), halo(C1-C6)alkyl (e.g., -CF3), halo(C1-C6)alkoxy (e.g., -OCF3), C1-C6 alkylthio, arylthio, amino, amino(C1-C6)alkyl, nitro,It is meant to be substituted with one or more substituents independently selected from O-carbamyl, N-carbamyl, O-thiocarbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C-carboxy, O-carboxy, acyl, cyanato, isocyanato, thiocyanato, isothiocyanato, sulfinyl, sulfonyl, sulfo, sulfino, sulfonate, and oxo (=O). Whenever a group is described as "optionally substituted," the group can be substituted with the above-mentioned substituents.

[0054] In some embodiments, the transposome complex is immobilized to the support via one or more polynucleotides (e.g., oligonucleotides), such as polynucleotides (oligonucleotides) that include a transposon end sequence. In some embodiments, the transposome complex can be immobilized via a linker added to the end of the transposon sequence, for example, by linking the transposase enzyme to a solid support. In some embodiments, both the transposase enzyme and the transposon polynucleotide (e.g., oligonucleotide) are immobilized to a solid support. When referring to the immobilization of a molecule (e.g., nucleic acid, enzyme) to a solid support, the terms "immobilized," "affixed," and "attached" are used interchangeably herein, and both terms are intended to encompass direct or indirect, covalent or non-covalent binding, unless otherwise indicated, whether explicitly or by context. In certain embodiments of the present disclosure, covalent attachment may be preferred, but generally all that is required is that the molecule (e.g., nucleic acid, enzyme) remain immobilized or bound to the support under the conditions for which the support is intended to be used, e.g., in applications requiring nucleic acid amplification and / or sequencing. In some cases, in bead-based tagmentation, the transposome may be bound to the bead surface via a ligand pair (e.g., affinity element and affinity binding partner).

[0055] Transposomes and transposases Transposon-based technologies include, for example, NEXTERA TM As exemplified in the workflow of the XT and FLEX DNA Sample Preparation Kits (Illumina, Inc.), it can be utilized to fragment DNA, where target nucleic acids (e.g., genomic DNA) are treated with a transposome complex that simultaneously tags and fragments ("tagmentation") the target, thereby creating a population of fragmented nucleic acid molecules tagged with unique adapter sequences at the ends of the fragments.

[0056] A transposition reaction is a reaction in which one or more transposons are inserted into a target nucleic acid at random or near-random sites. The components in a transposition reaction include a transposase (or other enzymes that can fragment and tag nucleic acids as described herein, such as integrase) and a transposon element that includes a double-stranded transposon end sequence that binds to the enzyme, and an adapter sequence that is attached to one of the two transposon end sequences. One strand of the double-stranded transposon end sequence is transferred to one strand of the target nucleic acid, and the complementary transposon end sequence strand is not transferred (i.e., the transposon sequence that is not transferred). The adapter sequence can include one or more functional sequences (e.g., primer sequences) if required or desired.

[0057] A "transposome complex" is composed of at least one transposase enzyme and a transposon recognition sequence. In some such systems, the transposase binds to the transposon recognition sequence to form a functional complex that can catalyze a transposition reaction. In some aspects, the transposon recognition sequence is a double-stranded transposon end sequence. The transposase, or integrase, binds to the transposase recognition site in the target nucleic acid and inserts the transposon recognition sequence into the target nucleic acid. In some such insertion events, one strand of the transposon recognition sequence (or end sequence) is transferred to the target nucleic acid and a cleavage event also occurs. Exemplary transposition procedures and systems that can be readily adapted for use with the transposases of the present disclosure are described, for example, in PCT Publication No. WO10 / 048605, U.S. Patent Publication No. 2012 / 0301925, U.S. Patent Publication No. 2012 / 13470087, or U.S. Patent Publication No. 2013 / 0143774, each of which is incorporated by reference in its entirety herein.

[0058] Exemplary transposases that can be used with certain embodiments provided herein include (or are encoded by): Tn5 transposase (see Reznikoff et al., Biochem. Biophys. Res. Commun. 2000, 266, 729-734), Vibrio harveyi (the transposase characterized by Agilent and used in their SureSelect QXT product), MuA transposase containing R1 and R2 end sequences and Mu transposase recognition sites (Mizuuchi, K., Cell, 35: 785, 1983; Savilahti, H, et al., EMBO J., 14:4893, 1995), Staphylococcus aureus Tn552 (Colegio, O. et al., J. Bacteriol., 183:2384-8, 2001; Kirby, C. et al., Mol. Microbiol., 43:173-86, 2002), Ty1 (Devine & Boeke, Nucleic Acids Res., 22:3765-72, 1994 and PCT Publication No. WO95 / 23875), transposon Tn7 (Craig, NL, Science, 271:1512, 1996; Craig, NL, Curr. Top. Microbiol. Immunol., 204:27-48, 1996), Tn / O and IS10 (Kleckner N. et al., Curr. Top. Microbiol. Immunol., 204:49-82, 1996), Mariner transposase (Lampe, DJ et al., EMBO J., 15:5470-9, 1996), Tc1 (Plasterk, RH, Curr. Top. Microbiol. Immunol., 204:125-43, 1996), P elements (Gloor, GB, Methods Mol. Biol., 260:97-114, 2004), Tn3 (Ichikawa & Ohtsubo, J. Biol. Chem., 265:18829-32, 1990), bacterial insertion sequences (Ohtsubo & Sekine, Curr. Top. Microbiol. Immunol. 204:1-26, 1996), retroviruses (Brown et al., Proc. Natl. Acad. Sci. USA, 86:2525-9, 1989), and yeast retrotransposons (Boeke & Corces, Ann. Rev. Microbiol. 43:403-34, 1989). More examples include IS5, Tn10, Tn903, IS911, and engineered versions of transposase family enzymes (Zhang et al., (2009) PLoS Genet. 5:e1000689. Epub Oct. 16; Wilson C. et al. (2007) J. Microbiol. Methods 71:332-5). The methods described herein can also include combinations of transposases rather than just a single transposase.

[0059] In some embodiments, the transposase is Tn5, MuA, or Vibrio harveyi transposase, or an active mutant thereof. In other embodiments, the transposase is a Tn5 transposase or an active mutant thereof. In some embodiments, the Tn5 transposase is a hyperactive Tn5 transposase (see, e.g., Reznikoff et al., PCT Publication No. WO2001 / 009363, U.S. Patent Nos. 5,925,545, 5,965,443, 7,083,980, and 7,608,434, and Goryshin and Reznikoff, J. Biol. Chem. 273:7367, 1998), or an active mutant thereof. In some aspects, the Tn5 transposase is a Tn5 transposase as described in PCT Publication No. WO2015 / 160895 (herein incorporated by reference). In some embodiments, the Tn5 transposase is a fusion protein. In some embodiments, the Tn5 transposase fusion protein comprises a fused elongation factor Ts (Tsf) tag. In some embodiments, the Tn5 transposase is a hyperactive Tn5 transposase comprising mutations at amino acids 54, 56 and 372 relative to the wild-type sequence. In some embodiments, the hyperactive Tn5 transposase is a fusion protein, optionally wherein the fused protein is an elongation factor Ts (Tsf). In some embodiments, the recognition site is a Tn5-type transposase recognition site (Goryshin and Reznikoff, J. Biol. Chem., 273:7367, 1998). In one embodiment, a transposase recognition site that forms a complex with a hyperactive Tn5 transposase is used (e.g., EZ-Tn5 TM transposase, Epicentre Biotechnologies, Madison, Wis.).

[0060] In some embodiments, the transposome complex is a dimer of two molecules of transposase. In some embodiments, the transposome complex is a homodimer, where the two molecules of transposase are each bound to a first and a second transposon of the same type (e.g., the sequences of the two transposons bound to each monomer are the same, forming a "homodimer"). In some embodiments, the compositions and methods described herein use two populations of transposome complexes. In some embodiments, the transposase in each population is the same. In some embodiments, the transposome complex in each population is a homodimer, where the first population has a first adapter sequence in each monomer and the second population has a different adapter sequence in each monomer.

[0061] In some embodiments, the transposase is a Tn5 transposase. In some embodiments, the transposase complex comprises a transposase (e.g., Tn5 transposase) dimer comprising a first and a second monomer. Each monomer comprises a first transposon and a second transposon, where the first transposon comprises a first transposon end sequence and a first adaptor sequence at its 3' end (where the adaptor sequences in each monomer of the dimer are the same or different), and the second transposon comprises a second transposon end sequence that is at least partially complementary to the first transposon end sequence. In some embodiments of the 5' cleavable linker aspect, the first transposon comprises a cleavable linker connected to an affinity element at its 5' end. In some embodiments of the 3' linker aspect, the second transposon comprises a linker (optionally cleavable) connected to an affinity element at its 3' end. Thus, in a preferred embodiment, one transposon from each monomer comprises an affinity element. However, in some embodiments, only one of the two monomers contains an affinity element.

[0062] Adapter sequences In any of the embodiments of the method described herein, the first transposon comprises a first adapter sequence. In some embodiments, a secondary adapter is added to the tagged fragment as described herein using a secondary adapter carrier, the secondary adapter carrier comprising a primer sequence and a secondary adapter sequence. The adapter sequence may comprise one or more functional sequences selected from the group consisting of a universal sequence, a primer sequence, an index sequence, a capture sequence, a barcode sequence (e.g., used for counting or error correction), a cleavage sequence, a sequencing-related sequence, and combinations thereof. In some embodiments, the adapter sequence comprises a primer sequence. In other embodiments, the adapter sequence comprises a primer sequence and an index sequence or a barcode sequence. The primer sequence may also be a universal sequence. This disclosure is not limited to the type of adapter sequence that may be used, and those skilled in the art will recognize additional sequences that may be useful for library preparation and next-generation sequencing.

[0063] The adaptor sequence (e.g., the first adaptor sequence) transferred to the 5' end of the nucleic acid fragment by the tagmentation reaction can include, for example, a universal sequence. A universal sequence is a region of nucleotide sequence common to two or more nucleic acid fragments. Optionally, the two or more nucleic acid fragments also have a region of sequence difference. A universal sequence that can be present in different members of a plurality of nucleic acid fragments can allow the duplication or amplification of a plurality of different sequences using a single universal primer that is complementary to the universal sequence.

[0064] In some embodiments, the compositions and methods described herein use two populations of transposome complexes. In some embodiments, each population comprises an adapter sequence with a different primer sequence. In some embodiments, the first population comprises an A14 primer sequence, and the second population comprises a B15 primer sequence.

[0065] Affinity elements and affinity binding partners An affinity element, as used herein, is a moiety that can be used to bind, covalently or non-covalently, to an affinity binding partner. In some aspects, the affinity element is on the transposome complex and the affinity binding partner is on a solid support.

[0066] In some embodiments, the affinity element can bind or is non-covalently bound to an affinity binding partner on a solid support, thereby non-covalently binding the transposome complex to the solid support. In such embodiments, the affinity element includes or is, for example, biotin, and the affinity binding partner includes or is avidin or streptavidin. In other embodiments, the affinity element / binding partner combination includes or is FITC / anti-FITC, digoxigenin / digoxigenin antibody, or hapten / antibody. Further suitable affinity pairs include, but are not limited to, dithiobiotin-avidin, iminobiotin-avidin, biotin-avidin, dithiobiotin-succinylated avidin, iminobiotin-succinylated avidin, biotin-streptavidin, and biotin-succinylated avidin.

[0067] In some embodiments, the affinity element can be bound to the affinity binding partner through a chemical reaction or covalently bound by reaction with an affinity binding partner on the solid support, thereby covalently binding to the transposome complex on the solid support. In some aspects, the affinity element / binding partner combination includes or is an amine / carboxylic acid (e.g., coupled under conditions known to those skilled in the art via standard peptide coupling reactions (e.g., EDC or NHS-mediated coupling)). Reaction of the two components links the affinity element and the binding partner through an amide bond. Alternatively, the affinity element and the binding partner can be two click chemistry partners (e.g., an azide / alkyne, which reacts to form a triazole linkage).

[0068] Cleavable Linkers The ability to break the bond that connects two molecular entities can be an effective tool to collapse the possibility of genome-wide off-target capture during the first hybridization, reducing the capture of off-target hybridization products. As defined herein, a cleavable linker is a molecule that has two functional heads that are connected together through a cleavable bond. The two functional heads serve to connect the linker to another moiety; in this case, the cleavable linker connects the 5' end of the first transposon sequence to the affinity element. An overview of cleavable linkers, classified according to their cleavage conditions and biological applications, is listed by Wagner et al., Bioorg. Med. Chem. 20, 571-582 (2012), which is incorporated herein by reference.

[0069] As used herein, a cleavable linker is a linker that can be cleaved through chemical or physical means (such as, for example, photolysis, chemical cleavage, thermal cleavage, or enzymatic cleavage). In some embodiments, the cleavage can be by biochemical, chemical, enzymatic, nucleophilic, reduction-sensitive agents, or other means.

[0070] In some embodiments, cleavable linker may comprise nucleotide or nucleotide sequence that can be fragmented by various means.For example, cleavable linker may comprise restriction endonuclease site; at least one ribonucleotide that can be cleaved by RNAse; nucleotide analog that can be cleaved in the presence of certain chemical agents; diol linkage that can be cleaved by treatment with periodate (for example); disulfide group that can be cleaved by chemical reducing agent; cleavable portion that can be susceptible to photochemical cleavage; and peptide that can be cleaved by peptidase enzyme or other suitable means.See, for example, U.S. Patent Publication Nos. 2012 / 0208705 and 2012 / 0208724, and PCT Publication No. WO 2012 / 061832 (each of which is incorporated by reference in its entirety).

[0071] Photocleavable (PC) linkers have been used in a variety of applications such as photocleavage-induced purification, protein engineering, photoactivation of compounds and biomolecules, and photocleavable mass tagging for multiplex assays. PC linkers can contain photolabile functional groups that are cleavable by UV light of a specific wavelength (300-350 nm). The PC linker can, for example, contain a 10-atom unit that can be cleaved when exposed to UV light in the appropriate spectral range. Such photocleavable linkers and phosphoramidite reagents are available from Integrated DNA technologies (IDT), Ambergen, and Glen Biosciences. Photocleavable nucleotide compositions are commercially available from Biosciences Research. The use of photocleavable nucleotide compositions is described in detail in U.S. Patent Nos. 7,057,031, 7,547,530, 7,897,737, 7,964,352 and 8,361,727, which are incorporated by reference in their entireties.

[0072] In some embodiments, cleavage is mediated by an enzyme by incorporating a cleavable nucleotide or nucleobase into the cleavable linker. Examples of such nucleobases or nucleobase moieties include, but are not limited to, uracil, uridine, 8-oxo-guanine, xanthine, hypoxanthine, 5,6-dihydrouracil, 5-methylcytosine, thymidine-dimer, 7-methylguanosine, 8-oxo-deoxyguanosine, xanthosine, inosine, deoxyinosine, dihydrouridine, bromodeoxyuridine, uridine, 5-methylcytidine, deoxyuridine, 5,6-dihydroxythymine, thymine glycol, 5-hydroxy-5-methylhydanton, uracil glycol, 6-hydroxy-5,6-dihydrothymine, methyl tartronyl urea (1,2), or an abasic site.

[0073] In some embodiments, the cleavable linker comprises a sufficient number of cleavable nucleotides to allow complete cleavage. In some embodiments, the linker comprises 1-10 cleavable nucleotides. In some embodiments, the cleavable linker comprises at least one cleavable nucleotide. In some embodiments, the linker comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 cleavable nucleotides. In preferred embodiments, the cleavable linker comprises one or more uracil nucleotides and optionally other standard DNA bases. In some embodiments, an additional enzymatic step after PCR cleaves the cleavable linker at the cleavable nucleotide or nucleoside position. Examples of such enzymes include, but are not limited to, uracil DNA glycosylase (UDG (also called uracil-N-glycosylase or UNG)), formamidopyrimidine DNA glycosylase (Fpg), RNaseH, Endo III, Endo IV, Endo V, Endo VIII, Klenow, or apyrase. In some embodiments, a blend of enzymes is used that includes an enzyme that cleaves uracil bases in nucleic acids and an AP nuclease. The effective concentration of the enzymes is 0.025 U / μl to 10 U / μl. In a preferred embodiment, the enzyme blend is uracil DNA glycosylase and Endo IV. Commercially available enzyme mixtures for use in the methods described herein include UDEM (Epicentre Biotechnologies). In yet another embodiment, the enzyme blend is uracil DNA glycosylase and Endo VIII (commercially available as USER (New England Biolabs) or Uracil Cleavage System (Sigma Aldrich)). The cleavage leaves a 5' affinity element (e.g., a biotin moiety) on the short oligonucleotide that can be removed by a number of methods known to those of skill in the art, for example, during nucleic acid purification, such as removal of target nucleic acid using bead-based methodologies that leave small oligonucleotides uncaptured. The cleavage breaks the linkage between the affinity element (e.g., biotin) and the 5' tagged target fragment. In a preferred embodiment, the cleavable linker is attached adjacent to the 5' end of the transposon end sequence of the transposon duplex. In some embodiments, the cleavable linker is linked to biotin, hi other embodiments, the biotin is attached to a streptavidin coated bead.

[0074] Transposome complex and transposon with 3' linker In other aspects, the linker is connected to the 3' end of the second transposon, where the linker can connect the second transposon to a solid support. When the first and second transposons are part of a transposome complex, the linker serves to connect the complex to a solid support. In such aspects, the first end of the linker is attached to the 3' end of the second transposon, and the second end of the linker is attached to an affinity element. The affinity element can be attached (covalently or non-covalently) to an affinity binding partner on a solid support. In some aspects, the affinity element is attached (covalently or non-covalently) to an affinity binding partner on a solid support to provide a transposome complex bound to a solid support. In some aspects, the linker is a cleavable linker. These complexes are 3'-linker transposome complexes and 3'-linker transposome complexes bound to a support. In some embodiments, the affinity element is biotin and the affinity binding partner is streptavidin.

[0075] In one embodiment, the linker is covalently linked to the 3' end of the second transposon. In some embodiments, the linker is covalently linked to the 3' end of the second transposon end sequence. For example, the linker described herein can be covalently and directly linked to the 3' end hydroxyl group of the second transposon, thus forming an -O-linkage, or can be covalently linked through another group (e.g., phosphate or ester). Alternatively, the linker described herein can be covalently linked to the phosphate group of the second transposon or the second transposon end sequence (e.g., can be covalently linked to the 3' hydroxyl through a phosphate group, thus forming an -OP(O)3-linkage).

[0076] In some embodiments, the transposome complexes described herein are immobilized to a solid support via a linker. In some such embodiments, the affinity element is biotin and the solid support comprises streptavidin. In some further embodiments, the solid support comprises or is a bead. In one embodiment, the bead is a paramagnetic bead.

[0077] In some embodiments, the linker and affinity element have the structure of formula (I): [ka] where: AE is an affinity element; Y is C 2-6 is alkylene; X 1 , O, NR 1 , or S; Here, R 1 is H or C 1-10 is alkyl; n is an integer selected from the group consisting of 1, 2, 3, 4, 5, and 6; X 2 is O, CH2 or S; R a is H or -OH; and Z is R a is H, or R a is H or OH, then CH2; where [ka] marks the point of attachment to the second transposon.

[0078] In some embodiments of formula (I), AE is an optionally substituted biotin or an amino group. In other embodiments, AE is an optionally substituted biotin. In such embodiments, biotin is 1-4 Optionally substituted with alkyl. In another embodiment, AE is biotin.

[0079] In some embodiments of Formula (I), Y is C 2-6 In another embodiment, Y is C 2-5 In another embodiment, Y is C 2-4 In another embodiment, Y is C 2-3 In another embodiment, Y is an alkylene. In another embodiment, Y is an unbranched alkylene. In another embodiment, Y is a C2 alkylene. In another embodiment, Y is a C3 alkylene. In another embodiment, Y is a C4 alkylene. In another embodiment, Y is ethylene. In another embodiment, Y is propylene. In another embodiment, Y is butylene.

[0080] In some embodiments of formula (I), X 1 is NR 1 where R 1 is H or C 1-10 In some such embodiments, R 1 is H. In some embodiments, R 1 is C 1-3 In another embodiment, X is alkyl. 1 is O. In other embodiments, X 1 is S.

[0081] In some embodiments of Formula (I), n is 1. In other embodiments, n is 2. In other embodiments, n is 3. In other embodiments, n is 4.

[0082] In some embodiments of formula (I), X2 is CH2. In some other embodiments, X 2 is O. In other embodiments, X 2 is S.

[0083] In some embodiments of Formula (I), R a is H. In other embodiments, R a is -OH.

[0084] In some embodiments of Formula (I), Z is absent and R a is H. In some embodiments, Z is CH and R a is H. In some embodiments, Z is CH and R a is OH.

[0085] In some embodiments, the linker and affinity element have the structure of formula (I'): [ka] where AE, Y, X 1 , n, X 2 is defined as described herein for formula (I), and Z is absent or CH2.

[0086] In some embodiments, the linker and affinity element have the structure of Formula (Ia): [ka] where X 1 , n, X 2 , R a and Z are defined as described herein with respect to formula (I). In some embodiments, R a is H.

[0087] In some embodiments, the linker and affinity element have the structure of Formula (Ib): [ka] where AE is as defined herein for formula (I); and n is 1 or 2.

[0088] In some aspects of formula (Ib), AE is an optionally substituted biotin or an amino group. In some embodiments, AE is biotin.

[0089] In some embodiments, the linker and affinity element have the structure of formula (Ic): [ka] where AE is as defined herein for formula (I); 2 is O or CH2; n is 1 or 2; and Z is absent or CH2.

[0090] In some embodiments of formula (Ic), AE is an optionally substituted biotin or amino group. In some embodiments, AE is biotin. In some embodiments, X 2 is O. In some embodiments, X 2 In some embodiments, n is 1. In some embodiments, n is 2. In some embodiments, Z is absent. In some embodiments, Z is CH2. In some embodiments, n is 1 and X 2 In some embodiments, n is 1 and X is O and Z is absent. 2 is CH2 and Z is CH2.

[0091] In some embodiments, the linker and affinity element are selected from the group consisting of: [ka] It has a structure selected from the following:

[0092] In some embodiments, the linker and affinity element have the structure (I(c)).

[0093] In some embodiments, the adapter sequence comprises a primer sequence. In some embodiments, the primer sequence is an A14 or B15 primer sequence. In some embodiments, the primer sequence is a P5 or P7 primer sequence. In some embodiments, the transposase is a dimer, and each monomer is bound to a transposon duplex having an adapter sequence as described herein, where the adapter sequence in each monomer is the same. In embodiments where the transposase is a dimer, one or both monomers comprise a linker that connects the transposome complex to a solid support. Each monomer comprises a first transposon having an adapter sequence.

[0094] solid support The terms "solid surface", "solid support" and other grammatical equivalents refer to any material that is suitable or can be modified to be suitable for binding transposome complexes. As will be recognized by those skilled in the art, the number of possible substrates is multiple. Possible substrates include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethane, TEFLON®, etc.), polysaccharides, nylon or nitrocellulose, ceramics, resins, silica or silica-based materials (including silicon and modified silicon), carbon, metals, inorganic glass, plastics, fiber optic bundles, beads, paramagnetic beads, and various other polymers.

[0095] In some such embodiments, the transposome complex is immobilized on the solid support via a linker as described herein. In some further embodiments, the solid support comprises or is a tube, a well of a plate, a slide, a bead, or a flow cell, or a combination thereof. In some further embodiments, the solid support comprises or is a bead. In one embodiment, the bead is a paramagnetic bead.

[0096] In the methods and compositions presented herein, the transposome complex is immobilized on a solid support. In one embodiment, the solid support is a bead. Suitable bead compositions include, but are not limited to, plastic, ceramic, glass, polystyrene, methylstyrene, acrylic polymers, paramagnetic materials, thoria sol, carbon graphite, titanium dioxide, latex or cross-linked dextran (e.g., Sepharose), cellulose, nylon, cross-linked micelles and TEFLON®, and any other materials outlined herein for solid supports. In certain embodiments, the microsphere is a magnetic microsphere or bead (e.g., a paramagnetic particle, sphere or bead). The bead does not have to be spherical; irregular particles may be used. Alternatively or additionally, the bead may be porous. Bead sizes range from nanometers (e.g., 100 nm) to millimeters (e.g., 1 mm), with beads from about 0.2 microns to about 200 microns being preferred, and about 0.5 to about 5 microns being particularly preferred, although in some embodiments smaller or larger beads may be used. The beads may be coated with an affinity binding partner, for example, the beads may be streptavidin coated. In some embodiments, the beads are streptavidin coated paramagnetic beads, such as Dynabeads MyOne Streptavidin C1 beads (Thermo Scientific catalog number 65601), Streptavidin MagneSphere Paramagnetic particles (Promega catalog number #Z5481), Streptavidin Magnetic beads (NEB catalog number #S1420S) and MaxBead Streptavidin (Abnova catalog number U0087). The solid support may also be a slide, such as a flow cell or other slide modified so that transposome complexes can be immobilized thereon.

[0097] In some embodiments, the affinity binding partner is present on the solid support or beads at a density of from about 1000 to about 6000 pmol / mg, or from about 2000 to about 5000 pmol / mg, or from about 3000 to about 5000 pmol / mg, or from about 3500 to about 4500 pmol / mg.

[0098] In one embodiment, the solid surface is the inner surface of a sample tube. In one example, the sample tube is a PCR tube. In another embodiment, the solid surface is a capture membrane. In one example, the capture membrane is a biotin capture membrane (e.g., available from Promega Corporation). In another example, the capture membrane is filter paper. In some embodiments of the present disclosure, the solid support is composed of an inert substrate or matrix (e.g., glass slide, polymer beads, etc.), and is functionalized, for example, by applying a layer that allows for covalent binding to molecules (e.g., polynucleotides) or coating with an intermediate material that contains reactive groups. Examples of such supports include, but are not limited to, polyacrylamide hydrogels supported on an inert substrate (e.g., glass, particularly polyacrylamide hydrogels as described in WO2005 / 065814 and US2008 / 0280773, the contents of which are incorporated herein by reference in their entirety). Methods for tagmenting (fragmenting and tagging) DNA on solid surfaces for the construction of tagmented DNA libraries are described in WO2016 / 189331 and US2014 / 0093916A1, which are incorporated by reference herein in their entireties.

[0099] Some further embodiments of the present disclosure relate to a solid support comprising a transposome complex immobilized thereon as described herein, wherein the linker and affinity element have the structure of formula (I), (I'), (Ia), (Ib), (Ic), (I(a)), (I(b)), or (I(c)) as described herein. In some embodiments, the transposome complex described herein is immobilized to the solid support via an affinity element. In some such embodiments, the solid support comprises streptavidin as an affinity binding partner, and the affinity element is biotin. In some further embodiments, the solid support comprises or is a bead. In one embodiment, the bead is a paramagnetic bead.

[0100] In some embodiments, transposome complexes are immobilized on a solid support (e.g., beads) at a specific density or density range. The density of the complexes on the beads, as the term is used herein, refers to the concentration of the transposome complexes in solution during the immobilization reaction. The complex density assumes that the immobilization reaction is quantitative. Once the complexes are formed at a specific density, the density remains constant for a batch of transposome complexes bound to the surface. The resulting beads can be diluted, and the resulting concentration of the complexes in the diluted solution is the desired density of the beads divided by the dilution factor. Diluted bead stocks retain the complex density from their preparation, but the complexes are present at a lower concentration in the diluted solution. The dilution step does not change the density of the complexes on the beads, so it affects the library yield but not the insert (fragment) size. In some embodiments, the density is between about 5 nM and about 1000 nM, or between about 5 and 150 nM, or between about 10 nM and 800 nM. In other embodiments, the density is about 10 nM, or about 25 nM, or about 50 nM, or about 100 nM, or about 200 nM, or about 300 nM, or about 400 nM, or about 500 nM, or about 600 nM, or about 700 nM, or about 800 nM, or about 900 nM, or about 1000 nM. In some embodiments, the density is about 100 nM. In some embodiments, the density is about 300 nM. In some embodiments, the density is about 600 nM. In some embodiments, the density is about 800 nM. In some embodiments, the density is about 100 nM. In some embodiments, the density is about 1000 nM.

[0101] In some embodiments, the solid support is a bead or a paramagnetic bead, and greater than 10,000, 20,000, 30,000, 40,000, 50,000, or 60,000 transposome complexes are attached to each bead.

[0102] Different densities of transposome complexes bound to the solid support result in fragments of different lengths (e.g., different insert sizes). For example, as shown in Figures 7A, 7B, and 7C, different complex densities result in different insert sizes. Insert sizes can be from about 50 bp to about 1000 bp, or from about 100 to about 600 bp, or from about 175 to about 200 bp, or about 500 bp.

[0103] Methods for preparing modified oligonucleotides and immobilized transposome complexes The present disclosure further provides a method for preparing modified oligonucleotides, transposome complexes, and transposome complexes bound to solid support as described herein.In some aspects, such methods include treating transposase with a first and a second transposon as described herein under suitable conditions to form a complex.The method for preparing transposome complexes bound to solid support includes incubating a transposome complex as described herein with a solid support that contains an affinity binding partner under conditions sufficient for the affinity element to bind (covalently or non-covalently) to the affinity binding partner.

[0104] In some embodiments, there is a method for preparing modified oligonucleotides. In some aspects, methods for preparing modified oligonucleotides with linkers connected to affinity elements are known in the art. Certain methods contemplated herein include reacting a linker (or cleavable linker) reagent that includes a first reactive functional group (L-FG1) with a nucleotide that includes a second reactive functional group (N-FG2), whereby the first and second reactive functional groups react to form a linker-nucleotide product (L-(CB)-N) with a covalent bond (CB) between the linker and the nucleotide. In some embodiments, the linker reagent includes an AE moiety (AE-linker-FG1). In other embodiments, the linker reagent includes a portion of a linker structure, and AE is introduced through a second coupling reaction to generate a complete AE-linker structure.

[0105] The first reactive functional group can be, for example, a carboxyl, an activated carboxyl (e.g., an ester, an NHS ester, an acyl halide, an anhydride, etc.), an azide, an alkyne, a formyl, or an amino. In some embodiments, the first reactive functional group is an activated carboxyl, preferably an NHS ester.

[0106] The second reactive functional group can be present at any suitable position on the nucleotide. In some embodiments, the second reactive functional group is present at the 3' hydroxyl or 5' phosphate position of the nucleotide, either in place of or as a tether to a natural substituent (e.g., an alkylene or heteroalkylene group), or, in the case of a nucleotide hydroxyl, appended thereto via the phosphate group. In some embodiments, the second reactive functional group is C 2-10In some embodiments, the second reactive functional group comprises an -alkylamino group. In some embodiments, the second reactive functional group comprises a hexylamino group. In some embodiments, the second reactive functional group is -OP(O)3-(CH2)6-NH2. In some embodiments, the second reactive functional group is attached to the nucleotide via a phosphate tether through the 3' hydroxyl of the nucleotide.

[0107] The modified nucleotide can be part of the oligonucleotide prior to attachment of the linker, in which case the nucleotide can be, for example, at the 3' or 5' end of the oligonucleotide. Alternatively, the linker can be attached to the nucleotide first, and the modified nucleotide used as a starting material in synthesizing the oligonucleotide by standard means.

[0108] In some embodiments, the linker of formula (I) is attached to the 3' position of a nucleotide (e.g., cytidine). In some embodiments, the method for making a modified nucleotide comprises combining a compound of formula (II) and a compound of formula (III): [ka] where A, Y, n, and X 2 , R a and Z is as defined herein; -C(O)X 3 is an activated ester (e.g., an ester, an acyl halide, an ester anhydride, or an NHS ester); and X 4 is an -OH or -NH group; The method includes reacting a compound of formula (II) with a compound of formula (III) to form a compound of formula (I)]-nucleotide.

[0109] In some embodiments, the compound of formula (II) is AE-(CH2)4C(O)-O-NHS and the compound of formula (III) is H2N-(CH2)6-OP(O)(O -) O-nucleotide, and the product is AE-(CH2)4C(O)-NH-(CH2)6-OP(O)(O - In some embodiments, the phosphate is attached to the 3' hydroxyl group of the nucleotide (e.g., cytidine). In some embodiments, the compound of formula (I)-nucleotide (or AE-(CH2)4C(O)-NH-(CH2)6-OP(O)(O - )O-nucleotide) can be reacted with an additional nucleotide to form a [Formula (I)]-oligonucleotide (or AE-(CH2)4C(O)-NH-(CH2)6-OP(O)(O - In some embodiments, the second transposon forms a [Formula (I)]-oligonucleotide (or AE-(CH2)4C(O)-NH-(CH2)6-OP(O)(O - )O-oligonucleotide).

[0110] The present disclosure also relates to a method for preparing a transposome complex using the modified oligonucleotide described herein. Such a method comprises mixing a transposase, a first transposon, and a second transposon (as defined herein), where the first and second transposon end sequences are annealed to each other to form a transposome complex. As described herein, one of the first and second transposons comprises an affinity element (at the 5' end in the case of the first transposon; at the 3' end in the case of the second transposon). In some embodiments, the method further comprises binding the affinity element to a solid support that comprises an affinity binding partner. The binding can be performed before or after the formation of the transposome complex.

[0111] Preparation of sequencing fragments - Amplification of tagged fragments In some aspects, a method is provided for preparing sequencing fragments from target nucleic acid, comprising the steps of: providing a solid support comprising the transposome complexes described herein immobilized on the solid support as described herein; contacting the solid support with the target nucleic acid under conditions that fragment the target nucleic acid and link a first transposon to the 5' end of the fragment, thereby immobilizing the fragment on the solid support.In some aspects, the method further comprises amplifying the fragmented nucleic acid.In an embodiment, the fragmentation conditions are suitable for tagmentation by using transposome complexes to fragment and tag the target nucleic acid.

[0112] In some embodiments of the methods described herein, after fragmentation and tagging, the method further comprises removing the transposase from the 5'-tagged target fragment to provide an uncomplexed 5'-tagged target fragment. Removal of the transposase can be achieved under chemical conditions (e.g., treatment with a denaturing agent such as sodium dodecyl sulfate (SDS)). Such methods can further comprise generating a fully duplexed version of the 5'-tagged target fragment. The fully duplexed version can comprise removing the annealed (but unlinked) second transposon (AE-linker-second transposon) from the 5'-tagged target fragment and extending the 5'-tagged target fragment to generate a fully duplexed 5'-tagged target fragment. The generating can be achieved, for example, by heating the uncomplexed 5'-tagged target fragment to a temperature sufficient to selectively denature the second transposon, leaving the remaining duplexed region of the fragment intact. The extending step can be accomplished in the presence of dNTPs and a suitable polymerase. Alternatively, the generating step can be accomplished in one reaction by incubating the uncomplexed 5' tagged target fragment in the presence of single nucleotides (dNTPs) and a polymerase. In some embodiments, the incubating step includes heating at one or more temperatures sufficient to denature the annealed second transposon and extend the remaining duplex. In other embodiments, the polymerase is a strand-displacing polymerase, which serves to remove the second transposon and extend the remaining duplex to generate a fully duplexed 5' tagged target fragment. Suitable polymerases include KAPA HiFi, Pfu, and similar enzymes. Suitable polymerases include strand-displacing polymerases (e.g., Bst, Bsu Vent, Klenow, and similar enzymes).

[0113] In some aspects, the method further comprises amplifying the fully duplexed 5' tagged target fragment. The amplifying step can be performed by any suitable amplification method, such as polymerase chain reaction (PCR), rolling circle amplification (RCA), or multiple displacement amplification (MDA). In some embodiments, the amplifying step is performed by PCR. In some embodiments, the amplifying and extending steps are performed in one reaction step by reacting in the presence of dNTPs and a polymerase.

[0114] In some embodiments, the amplifying step serves to add one or more secondary adapter sequences to the fully duplexed, 5'-tagged target fragment to form a sequencing fragment. The amplifying step is accomplished by incubating the fully duplexed, 5'-tagged target fragment, including a primer sequence at each end, with a secondary adapter carrier, a single nucleotide, and a polymerase under conditions sufficient to amplify the target fragment and incorporate the secondary adapter carrier (or its complement), where the secondary adapter carrier includes a complement to a primer sequence and a secondary adapter sequence.

[0115] In some embodiments, the secondary adapter carrier comprises a primer sequence, an index sequence, a barcode sequence, a purification tag, or a combination thereof. In some embodiments, the secondary adapter carrier comprises a primer sequence. In some embodiments, the secondary adapter carrier comprises an index sequence. In some embodiments, the secondary adapter carrier comprises an index sequence and a primer sequence.

[0116] In some embodiments, the fully double-stranded 5' tagged target fragment comprises different primer sequences at each end.In such embodiments, each secondary adapter carrier comprises the complement of one of the two primer sequences.In some embodiments, the two primer sequences are A14 primer sequence and B15 primer sequence.

[0117] In some embodiments, multiple secondary adapters are added by amplification. In some embodiments, each secondary adapter carrier comprises one of two primer sequences. In some embodiments, each secondary adapter carrier comprises one of multiple index sequences. In some embodiments, the secondary adapter carrier comprises a secondary adapter with a P5 primer sequence and a secondary adapter with a P7 primer sequence.

[0118] In some embodiments, the sequencing fragment is deposited on a flow cell. In some embodiments, the sequencing fragment is hybridized to a complementary primer grafted to a flow cell or surface. In some embodiments, the sequence of the sequencing fragment is detected by array sequencing or next-generation sequencing (e.g., sequencing-by-synthesis).

[0119] P5 and P7 primers are used on the surface of commercially available flow cells sold by Illumina, Inc. for sequencing on various Illumina platforms. The primer sequences are described in U.S. Patent Publication No. 2011 / 0059865 A1, which is incorporated by reference in its entirety. Examples of P5 and P7 primers, which may be alkyne-terminated at the 5' end, are as follows: P5: AATGATACGGCGACCACCGAGAUCTACAC (SEQ ID NO: 1) P7: CAAGCAGAAGACGGCATACGAG*AT (SEQ ID NO: 2) and derivatives thereof.

[0120] In some examples, the P7 sequence includes a modified guanine at the G* position, e.g., 8-oxo-guanine. In other examples, the * indicates that the bond between the G* and the adjacent 3'A is a phosphorothioate bond. In some examples, the P5 and / or P7 primers include a non-natural linker. Optionally, one or both of the P5 and P7 primers can include a poly-T tail. The poly-T tail is generally located at the 5' end of the sequence shown above, e.g., between the 5' base and the terminal alkyne unit, but in some cases, can be located at the 3' end. The poly-T sequence can include any number of T nucleotides (e.g., 2-20). While P5 and P7 primers are shown as examples, it should be understood that any suitable amplification primer can be used within the examples shown herein.

[0121] In some embodiments, the amplifying step of the above methods comprises PCR or isothermal amplification. In some embodiments, the amplifying step of the above methods comprises PCR.

[0122] Description of the drawings FIG. 1 illustrates exemplary steps of a method for preparing transposome complexes and attaching them to a solid surface (e.g., beads) through affinity elements linked to the 5' end of a first transposon. In this example, two populations (130a and 130b) of annealed first and second transposons (oligonucleotides comprising annealed double-stranded and single-stranded regions comprising transposon end sequences) (wherein in each population, the first transposon comprises one of two adapter sequences and an affinity element (110, where * denotes affinity element) (e.g., biotin) at the 5' end), e.g., a plurality of biotinylated first and second transposons comprising two adapter sequences (e.g., primer sequences such as A14 and B15) are generated. As shown, the strand of the double-stranded transposon sequence transferred to the template nucleic acid is the first transposon, which has an affinity element (e.g., biotin). In step 115, each population of oligonucleotides (130a and 130b) is complexed with a transposase monomer (e.g., Tn5 (135)), typically in a separate reaction, to create two separate populations of transposome complexes (140), each with a different adapter sequence (e.g., primer sequences such as A14 and B15). After the two populations of complexes are formed, they are immobilized (120) on a substrate (in this example, beads). In some embodiments, the two populations are combined prior to immobilization, resulting in a solid surface or bead that contains complexes from each population. In other embodiments, the two populations are immobilized separately, resulting in two solid surfaces or beads, each containing one of the two complex types. After transposome complex formation, the transposomes 140 are bound to a surface 145 coated with an affinity binding partner (e.g., streptavidin).

[0123] FIG. 2 illustrates a tagmentation and library preparation process 200 on a bead surface after immobilization of transposomes using the 5′ linker strategy described herein. Shown in the process 200 are beads 205 with transposomes 140 bound to them. DNA 210 is added to the sample of beads. When the DNA 210 contacts the transposomes 140, the DNA is tagmented (fragmented and tagged) and bound to the beads 205 via the transposomes 140. The bound and tagmented DNA can be PCR amplified to generate a pool of bead-free amplicons 215. The PCR step can be used to incorporate secondary adapter sequences (e.g., primer sequences (e.g., P5 and P7)). The amplicons 215 can be transferred to the surface of a flow cell 220, for example, by grafting or hybridizing to complementary primers on the flow cell surface. A cluster generation protocol (e.g., a bridge amplification protocol or any other amplification protocol that can be used for cluster generation) can be used to generate a plurality of clusters 225 on the surface of the flow cell. The clusters are the clonal amplification products of the tagmented DNA. The clusters are now ready for the next step in the sequencing protocol. An example of the tagmentation process on the bead surface is described in detail in PCT Publication No. WO2016 / 189331, which is incorporated by reference in its entirety herein.

[0124] Figure 3 illustrates issues that can arise when using 5'-linked transposome complexes. Step 300 pictorially illustrates the tagmentation process of transposome complexes 140 immobilized on beads 305 with genomic DNA 315, followed by subsequent amplification and target enrichment, including capture of non-target nucleic acids. An immobilized library of tagmented genomic DNA is shown at 310. The streptavidin-coated capture beads with tagmented DNA can be washed (320) using a wash buffer (e.g., containing 5% SDS, 100 mM Tris-HCl pH 7.5, 100 mM NaCl, and 0.1% Tween 20), thereby denaturing the transposase from the transposome complexes. The supernatant can then be removed via magnetic capture of streptavidin-coated paramagnetic particles (e.g., beads) after a washing step, and the capture beads containing the immobilized tagmented library can be retained and further washed using 100 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.1% Tween 20. The bound oligonucleotides are extended at 330 to form bound duplexes with perfect complementarity.

[0125] At 340, target amplification proceeds via thermal cycling to amplify the tagmented DNA by methods known to those skilled in the art. For example, a solution of PCR reagents (e.g., a mixture including, at a minimum, PCR buffer, deoxy-nucleotides, divalent cations, and DNA polymerase) and additives required for efficient amplification can be added to the bead-containing solution, and the tagmented DNA bound to the capture beads can be amplified by thermal cycling (e.g., 10 thermal cycles), a methodology known to those skilled in the art. At 350, the amplified tagmented DNA can be optionally purified and eluted, for example, using a purification column (e.g., Zymo spin column). The amplified tagmented DNA can also be optionally purified using SPRI or Ampure XP beads (Beckman Coulter), and the purification method is not limited to this disclosure.

[0126] In step 360, the tagmentation library can be enriched using the NEXTERA Rapid Capture enrichment protocol (Illumina) or a protocol as described in any other target capture method. The biotinylated genomic fragments from the beginning of the library preparation are present in the post-amplification mixture (370) and can compete with the biotinylated target probes (380) and act as whole genome hybridization probes during target enrichment. The presence of these biotinylated genomic fragments at this stage can impair the efficiency of enrichment. In addition, biotinylated genomic fragments can be generated during PCR amplification by polymerase priming and extension of free biotinylated adapters that were not consumed in the tagmentation reaction, thereby adding additional off-target capture probes to the target enrichment step.

[0127] This disclosure provides several solutions to this problem. In one approach described herein, one or more cleavable linkers are included between the affinity element and the adapter sequence of the first transposon. Once tagmentation is completed and the tagmented nucleic acid is amplified, the cleavable linker can be cleaved, releasing the biotinylated moiety and minimizing or eliminating off-target capture. This modification drastically and surprisingly reduces off-target capture and improves enrichment compared to other bead-based tagmentation methodologies. Second, the affinity element is transferred to the 3' end of the second transposon and optionally attached through a cleavable linker.

[0128] Figure 4 pictorially illustrates the steps of a method 400 for fragmenting and tagging DNA using transposome complexes immobilized on a solid surface using a cleavable linker. With reference to Figure 4, steps 410, 420, 430, 440, and 450 are as described with respect to Figure 3 (310, 320, 330, 340, and 350, respectively), except that the biotinylated genomic fragments present in the post-amplification mixture (470) contain a cleavable linker (e.g., a linker containing one or more uracils). In step 460, biotin is cleaved from the genomic fragments by cleaving the linker using an appropriate cleavage agent. For the example of uracil, cleavage is accomplished with a uracil cleavage enzyme (e.g., Epicentre's Uracil DNA Excision Mix). During the enrichment step 480, the off-target genomic fragments are no longer biotinylated and therefore are not captured as the biotinylated target probes (490). In this manner, the method reduces off-target capture and increases the efficiency of target enrichment when compared to 5' ligation approaches without cleavable linkers.

[0129] A bead-based tagmentation approach using adapter sequences containing affinity elements such as biotin at the 5' end is shown in FIG. 5A. Briefly, two types of 5' end affinity elements, adapter oligonucleotides 501 and 502, are used to bind two populations of transposomes to the surface (e.g., one with A14 adapter sequence and one with B15 adapter sequence). ME and ME' are transposon end sequences. The tagmentation event creates 5' tagged fragments from the target nucleic acid (e.g., genomic DNA). Some of the fragments contain A14 at the 5' end of one strand and B15 at the 5' end of the other strand of the fragment, as shown. The fragments are extended and / or reacted by amplification (e.g., PCR), optionally in the presence of a secondary adapter carrier, to prepare complete duplexes or amplicons (optionally including secondary adapters (e.g., primer sequences such as P5 and P7 and / or index sequences as shown in the bottommost diagram)). If biotin / streptavidin is used, the affinity bond is broken during PCR, leaving biotinylated fragment amplicons in solution, which can complicate subsequent enrichment efforts. Alternatively, in FIG. 5B, the affinity element and linker bond is altered to the 3' position on the second transposon. In this case, the affinity element and linker are attached to the 3' end of the complementary transposon end sequence 503 (ME' sequence). In this configuration, the first transposon 501 and 502 do not contain affinity elements. With this process, the tagmentation event creates unlabeled fragmented genomic DNA. Because the first transposon (which lacks affinity elements) is transferred to the fragments, the affinity elements are only connected due to hybridization of the second transposon to the first transposon. The adapter sequences A14-ME, ME, B15-ME, ME', A14, B15, and ME are provided below: A14-ME: 5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3′ (SEQ ID NO: 3) B15-ME: 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3′ (SEQ ID NO: 4) ME': 5'-phos-CTGTCTCTTATACACATCT-3' (SEQ ID NO: 5) A14: 5′-TCGTCGGCAGCGTC-3′ (SEQ ID NO: 6) B15: 5′-GTCTCGTGGGCTCGG-3′ (SEQ ID NO: 7) ME: AGATGTGTATAAGAGACAG (SEQ ID NO: 8)

[0130] target nucleic acid The target nucleic acid can be of any type, including DNA, RNA, cDNA, etc. For example, the target nucleic acid can be in various states of purification, including purified nucleic acid. However, the nucleic acid does not need to be completely purified or purified at all, and can be part of a biological sample (e.g., raw sample lysate, bodily fluid, blood, plasma, or serum) or can otherwise be mixed with proteins, other nucleic acid species, other cellular components, and / or any other contaminating substances. In some embodiments, the biological sample includes a mixture of nucleic acids (e.g., DNA), proteins, other nucleic acid species, other cellular components, and / or any other contaminating substances, suitably present in the same proportions as found in vivo. For example, in some embodiments, the components are found in the same proportions as found in intact cells. Since the methods provided herein allow nucleic acids or DNA to be bound to a solid support through a tagmentation process, other contaminating substances can be removed by washing the solid support after tagmentation has occurred. The biological sample can include, for example, crude cell lysate or whole cells. For example, the crude cell lysate applied to the solid support in the methods provided herein need not have been subjected to one or more of the separation steps traditionally used to isolate nucleic acids from other cellular components.

[0131] Thus, in some embodiments, biological samples can include purified nucleic acids from any source, but also non-purified nucleic acids as found, for example, in blood, plasma, serum, lymph, mucus, sputum, urine, semen, cerebrospinal fluid, bronchial aspirate, feces, and macerated tissue, or lysates thereof, or any other biological specimen containing nucleic acid or DNA material. The target nucleic acid can be derived from a tissue sample, a tumor sample, a cancer cell, or a biopsy sample.

[0132] The target nucleic acid may be from any species or a mixture of species. For example, the target nucleic acid may be from a mammal (e.g., human, dog, cat, cow, pig, sheep, or other livestock), or from other species (e.g., fish, bacteria, viruses, fungi, or archaea). The nucleic acid may be from an environmental sample (e.g., soil or water).

[0133] In some embodiments, the target nucleic acid is DNA. In one such embodiment, the DNA is double-stranded. In some further embodiments, the double-stranded DNA comprises genomic DNA. In some other embodiments, the target nucleic acid is RNA or its derivative, or cDNA.

[0134] In some embodiments, biological sample (raw sample or extract) is processed to purify target nucleic acid before the tagmentation method described herein.In some embodiments, biological sample is raw sample or raw sample lysate (e.g., blood or saliva).In some embodiments, the processing method includes providing raw sample, raw sample lysate, or pre-processed sample (e.g., blood or saliva sample), mixing the sample with lysis buffer and proteinase K, incubating the mixture to lyse cells in the sample and release DNA from the cells, thereby providing target nucleic acid for the tagmentation method described herein.

[0135] Components in raw samples or raw sample lysates (e.g., blood) or additives in pre-processed samples (e.g., saliva collected in an Oragene collection tube) (stabilizing agents in the collection tube) may inhibit the tagmentation reaction. Thus, provided herein are methods for treating raw samples, raw sample lysates, or pre-processed samples to overcome this problem. In some embodiments, the methods include providing a raw sample, raw sample lysate, or pre-processed sample (e.g., blood or saliva sample), mixing the sample with a lysis buffer, proteinase K, and DNA purification beads (e.g., SPRI beads, beads containing carboxyl groups, where the beads are optionally magnetic beads), incubating the mixture to lyse cells in the sample and release DNA from the cells, thereby capturing the DNA on the DNA purification beads or SPRI beads, and separating the beads containing the captured DNA from the mixture. The separating step serves to remove potential tagmentation inhibitors present in the supernatant. The method further includes optionally washing the beads containing the captured DNA, and eluting the DNA from the beads to provide the target nucleic acid.

[0136] Sequencing Some of the methods provided herein include a method for analyzing nucleic acid. Such a method includes preparing a library of template nucleic acids of a target nucleic acid, obtaining sequence data from the library of template nucleic acids, and assembling a sequence representation of the target nucleic acid. In some embodiments, the methods described herein can be used in next-generation sequencing workflows, including but not limited to sequencing-by-synthesis (SBS). Exemplary SBS procedures, fluidics systems, and detection platforms that can be readily adapted for use with the nucleic acid libraries generated by the methods of the present disclosure are described, for example, in Bentley et al., Nature 456:53-59 (2008), WO 04 / 018497; US 7,057,026; WO 91 / 06678; WO 07 / 123744; US 7,329,492; US 7,211,414; US 7,315,019; US 7,405,281, and US 2008 / 0108082, each of which is incorporated by reference herein.

[0137] Some SBS embodiments include detection of protons released during incorporation of nucleotides into extension products. For example, sequencing based on detection of released protons can use electrical detectors and related technology available from Ion Torrent (Guilford, CT, a Life Technologies subsidiary) or separation methods and systems described in US 2009 / 0026082 A1; US ​​2009 / 0127589 A1; US ​​2010 / 0137143 A1; or US 2010 / 0282617 A1 (each of which is incorporated herein by reference).

[0138] Another useful sequencing technique is nanopore sequencing (see, e.g., Deamer et al. Trends Biotechnol. 18, 147-151 (2000); Deamer et al. Acc. Chem. Res. 35:817-825 (2002); Li et al. Nat. Mater. 2:611-615(2003), the disclosures of which are incorporated herein by reference). The methods described herein are not limited to any particular type of sequencing instrumentation used. EXAMPLES

[0139] The following examples are offered to illustrate, but not limit, the disclosure provided herein.

[0140] Example 1: Tagmentation on a solid surface using a linker with an enzymatically cleavable nucleotide Transposons were formed by annealing two sets of oligonucleotides (represented as any one of SEQ ID NOs: 9-11 (modified A14-ME) and any one of SEQ ID NOs: 12-14 (modified B15-ME)), which together base pair with a complementary mosaic end sequence (ME'; SEQ ID NO: 5) over a 19-base mosaic end (ME) sequence (SEQ ID NO: 8, shown in lowercase). Oligonucleotides represented by SEQ ID NOs: 9-14 were 5' biotinylated to allow for subsequent surface binding to streptavidin-coated paramagnetic beads. The annealed transposons were prepared by combining 50 μM of each biotinylated oligonucleotide with 50 μM ME' (SEQ ID NO: 5) in the presence of 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, and 25 mM NaCl, heated at 95° C. for 10 minutes, and cooled to room temperature for 2 hours. The annealed transposon was then mixed with transposase enzyme at a final concentration of 2 μM and incubated at 37° C. overnight.

[0141] Examples of cleavable linker sequences having cleavable nucleotide moieties are provided in SEQ ID NOs: 9-14. The sequences represented as SEQ ID NOs: 9-14 include a 19-base mosaic end (ME) sequence (shown in lower case) and lead 1 and lead 2 sequences, A14 and B15 (shown in italics). The sequences represented as SEQ ID NOs: 9 and 12 include a series of thymine residues (bold) followed by three uracil nucleotides (underlined). Similarly, the sequences represented as SEQ ID NOs: 10 and 13 include three uracil nucleotides 3' to the series of thymine residues. SEQ ID NOs: 11 and 14 include one uracil nucleotide after the series of thymine residues. As referred to herein, the thymine residues are part of the cleavable linker and serve to connect the biotin to the cleavable moiety 5' to the transposon and / or adapter sequence. In some embodiments, the cleavable linker includes 1-10 cleavable uracil nucleotides. In some embodiments, the cleavable linker includes at least one cleavable uracil nucleotide. In certain embodiments, the cleavable linker comprises 2, 3, 4, 5, 6, 7, 8, 9, or 10 cleavable uracil nucleotides. SEQ ID NO:8 is a 19-base mosaic end (ME) sequence and SEQ ID NO:5 is its complement. [ka]

[0142] Once the transposomes were formed, they were attached to streptavidin-coated beads. The beads were then washed with a dilute solution of transposomes in HT1 buffer (Illumina). HT1 contains high salt, which is required for biotin-streptavidin to bind to the beads. The beads and transposomes were incubated while mixing on a mixer for 1 hour. After mixing, the beads were resuspended in a storage buffer containing 15% glycerol and other buffering agents (e.g., Tris).

[0143] Tagmentation was then performed. For example, a tagmentation solution was added to the sample containing the immobilized transposomes and incubated at 55° C. for about 15 minutes. The tagmentation reaction included DNA (e.g., about 50 pg to 5 μg of DNA) and a tagmentation buffer. In one example, the tagmentation buffer includes the components necessary for the tagmentation reaction to occur (e.g., 10 mM NaCl ... (buffer containing Tris acetate (pH 7.6), 5 mM magnesium acetate, and 10% dimethylformamide) Immobilized libraries of tagged DNA fragments were generated.

[0144] Example 2: PCR amplification and enzymatic cleavage of tagmented DNA Streptavidin-coated capture beads (as described in Example 1) with tagmentation DNA on them were washed (e.g., three times) using a wash buffer containing 5% SDS, 100 mM Tris-HCl (pH 7.5), 100 mM NaCl, and 0.1% Tween 20, thereby denaturing the transposase enzyme of the transposome complex. The supernatant was removed after the wash step via magnetic capture of the streptavidin-coated paramagnetic particles (e.g., beads), retaining the beads containing the immobilized tagmentation library, and further washed using 100 mM Tris-HCl (pH 7.5), 100 mM NaCl, and 0.1% Tween 20.

[0145] Gap filling of the DNA fragments (filling the gap between the 5' end of the ME' sequence and the 3' end of the fragment (see, e.g., FIG. 5B)) was performed, for example, by adding NEM mix (NEXTERA Rapid Capture Kit, Illumina) and incubating at 72° C. for 3 minutes.

[0146] Target amplification via thermocycling was performed to amplify tagmentation DNA by methods known to those skilled in the art. In some examples, a solution of PCR reagents (e.g., a master mix (e.g., NEM mix (NEXTERA Rapid Capture Kit, Illumina)) containing at least PCR buffer, deoxynucleotides, divalent cations, DNA polymerase) and additives required for efficient amplification were added to the beads, and the tagmentation DNA bound to the beads was amplified by thermocycling (e.g., 10 thermal cycles).

[0147] The supernatant containing the amplified tagmentation DNA was removed from the reaction chamber and transferred to a new reaction chamber (e.g., tube, well, etc.). The amplified fragment mixture was treated with one or more enzymes that cleave the bases in the cleavable linker. Any one of a number of enzymes that break the known nucleotide backbone can be used to digest off-target products to prevent off-target hybridization to the genome. Examples of suitable enzymes include, but are not limited to, uracil DNA glycosylase (UDG (also called UNG)), formamide-pyrimidine DNA glycosylase (Fpg), RNAseH, Endo IV, Endo VIII, Klenow, or apyrase.

[0148] The amplified tagmentation DNA was purified using SPRI or Ampure XP beads (Beckman Coulter). The purification method is not limited to this disclosure. The tagmentation library can be enriched using the NEXTERA Rapid Capture enrichment protocol (Illumina) or the protocol described in any other target capture method. The enriched DNA library is now ready for sequencing.

[0149] Example 3: Lead enrichment using enzymatic cleavage of a uracil-containing cleavable linker Briefly, 50ng of NA12878 genomic DNA (Coriell Institute) was used for each condition tested. For control reactions, DNA was tagmented, libraries were prepared, and enriched following the NEXTERA Rapid Capture Enrichment (Illumina) protocol according to the manufacturer's recommendations. Uracil-containing cleavable linkers SEQ ID NO:9 and SEQ ID NO:13 were used.

[0150] Briefly, each 50 μL reaction contained 5× tagmentation buffer, 50 ng DNA, 5 μL of 250 nM transposome-conjugated Dynal paramagnetic beads (Life Technologies) with cleavable uracil linkers as set forth in SEQ ID NO:9 and SEQ ID NO:13. Reactions were incubated at 55° C. for 15 minutes, followed by the addition of 15 μL of Stop Tagment (ST) buffer, then incubated at room temperature for an additional 5 minutes. Samples were placed on a magnet and the supernatant was removed. The beads were resuspended in 50 μL NEM (Illumina) and incubated at 72° C. for 5 minutes, followed by cooling to 10° C. Samples were placed on a magnet, the supernatant was removed, and washed in HT2 wash buffer (Illumina).

[0151] PCR reactions were set up by adding 40 μL of EPM, 10 μL of each index primer (e.g., P5'-index-A14' and P7'-index-B15') and water. PCR amplification was performed as follows: 72°C, 3 min; 98°C, 30 sec, followed by 10 cycles of 98°C, 10 min; 65°C, 30 sec; 72°C, 60 sec. The PCR products were treated with 5 μL of USER enzyme mix (1 U / μl-NEB part number M5505L), incubated at 37°C for 30 min, and then size-selected using SPRI-based (Solid Phase Reversible Immobilization) paramagnetic AMPure XP beads (Beckman Coulter catalog number A63880) according to the manufacturer's recommendations. First, 100 μL of USER-treated PCR products were mixed with 55 μL water and 105 μL paramagnetic beads. The samples were placed off the magnet for 5 minutes, on the magnet for 5 minutes, then the supernatant was removed to a second size selection (250 μL supernatant + 30 μl paramagnetic beads). The beads were washed in 80% ethanol, air dried, and eluted in 25 μl RSB (Illumina).

[0152] Enrichment of the USER enzyme-treated and size-selected samples was performed according to the NEXTERA Rapid Capture Enrichment kit protocol using the TruSight One probe panel (Illumina) according to the manufacturer's recommendations (Illumina). The samples were sequenced on a HiSeq 2500 according to the manufacturer's recommendations (Illumina). [Table 1]

[0153] As shown in Table 1, solution-based tagmentation and enrichment (e.g., NEXTERA Rapid Capture) resulted in 70% read enrichment. Using transposomes attached to beads via a uracil-containing linker, but without enzymatic cleavage, the % read enrichment was significantly lower at 45%. However, when the uracil in the linker was cleaved via enzymatic cleavage, the enrichment increased to 67%, thereby restoring enrichment to the levels of non-immobilized, or solution-based, tagmentation and enrichment.

[0154] Example 4: 6-plex and 12-plex exome enrichment with and without enzymatic cleavage of uracil linkers The following examples show exome enrichment experiments using a five thymine (5T) linker, without enzymatic cleavage (2T3U+ENZ), compared to a two thymine and three uracil (2T3U) linker, in comparison to the TruSeq Rapid Exome Kit (Illumina).

[0155] The experimental procedure was as described for Example 3, except that 7.5 μL transposome-immobilized beads were used and the gap-filling step was omitted. Enrichment was performed using the TruSeq Rapid Exome kit (Illumina). Sequencing was performed on a HiSeq 2500 according to the manufacturer's recommendations (Illumina). [Table 2]

[0156] As shown in Table 2, only the 2T3U linker with enzymatic cleavage was detected by TruSeq We demonstrated enrichment metrics comparable to the Rapid Exome kit (Illumina) or solution-based NEXTERA using standard surface-based tagmentation with 5T residues.

[0157] Example 5: Comparison of 5'-biotinylated and 3'-biotinylated adaptor oligonucleotide methods One type of bead-based tagmentation approach uses an adapter sequence that is biotinylated at the 5' end as shown in FIG. 5A. Briefly, the 5' biotinylated adapter oligonucleotides 501 and 502 bind the transposome to the surface. The tagmentation event creates 5' biotinylated, fragmented total genomic DNA that can contaminate the subsequent enrichment step. In one embodiment, the attachment of biotin is changed to the 3' position on the complementary strand (second transposon) to bind the transposome to the surface as shown in FIG. 5B. Briefly, the oligonucleotides 501 and 502 do not contain biotin. In this example, biotin is attached to the transposon end sequence 503 on the complementary strand (ME' sequence). In this configuration, the tagmentation event creates biotin-free genomic DNA fragments.

[0158] In yet another embodiment, a linker is between the 3' oligonucleotide 503 and the biotin. This may help reduce any steric hindrance for possible transfer activity on the solid surface.

[0159] The following example shows the use of 3' biotinylated oligonucleotides with linkers of formula (I(a)) (glycerol type linkers) in the preparation of sequencing libraries. As a control reaction, DNA was tagmented, libraries were prepared, and enriched according to the manufacturer's recommendations (Illumina) following the NEXTERA Rapid Capture Enrichment protocol. The experimental protocol described in Example 3 was followed, except that the tagmented and amplified DNA was enriched using the Xgen Lockdown Hybridization Capture Kit protocol (Integrated DNA Technologies, IDT) using an exome panel, following the manufacturer's recommended protocol. Essentially, less than optimal enrichment was observed overall, since suboptimal blocking oligonucleotides were used as substitutes for the recommended universal blocking oligonucleotides provided in the Xgen lockdown kit. However, the focus of the experiment is not to require optimal blocking probes, but only to be able to observe measurable changes in the focus of the experiment. Suboptimal blocking oligonucleotides are not expected to affect the focus of the experiment. [Table 3]

[0160] As seen in Table 3, the 5' biotin and uracil linker + enzymatic cleavage showed significantly lower enrichment compared to the control and 3' biotin (with or without linker). The lower read enrichment associated with the 5' biotin and uracil linker + enzymatic cleavage method may be the result of incomplete cleavage by the enzyme mix. Experiments with the 3' linkage were shown to achieve read enrichment comparable to the solution-based control.

[0161] Example 6: Preparation of P-biotinylated beads for small inserts (150-200 bp) Step 1. Transposon annealing A14-ME and B15-ME were each annealed to ME'-linker-biotin oligo (preparation discussed below) resulting in two double stranded complexes, both with mosaic ends (ME) specifically recognized by the transposase and A14 or B15 sequences used in PCR to add secondary adapters. The A14-ME, B15-ME, and ME' oligos were resuspended to 200 nM. In a 96 well PCR plate, the preparations shown in Table 4 below were added to two wells (one well with A14:ME' and one well with B15-ME'). The well plate was placed in a thermal cycler for 10 minutes at 95°C, then removed from the thermal cycler and placed on the bench at room temperature for 2 hours. [Table 4]

[0162] Step 2. Transposome formation Tn5 transposase was added to the above annealed transposon, forming transposome complexes containing A14-ME / ME'-linker-biotin and B15-ME / ME'-linker-biotin complexes. The annealed oligos prepared from the previous step were used to set up the following reactions in a 96-well PCR plate: one well for A14-ME and one well for B15-ME. Each well was incubated overnight at 37°C in a thermal cycler to provide two populations of transposome complexes; the contents of the two wells were then mixed together. After the mixing step, approximately 220 μL was removed and added to another well. Approximately 220 μL of standard storage buffer (440 μL total) was added. [Table 5]

[0163] Step 3. Streptavidin Bead Loading The transposome complexes formed above containing biotin linkages were added to streptavidin beads. The density of the complexes on the beads can be adjusted to control the insert size in the tagmentation product. The streptavidin beads were mixed thoroughly. Approximately 200 μL of streptavidin beads were placed in a 1.5 ml tube and placed on a tube magnet. The beads were washed twice with 1 mL HT1, then the beads were resuspended and spun down between washes. After the second wash, the beads were thoroughly resuspended in 600 μL of HT1. 400 μL of the transposome complexes made above were added to the tube with HT1. The mixture was mixed on a rotary mixer for 1 hour, placed on a magnet, and the supernatant was removed. The mixture was resuspended in 500 μL of 15% standard storage buffer. The beads were loaded in the presence of 1000 nM transposome complex, and the resulting 1000 nM density complex was diluted and stored in solution to a concentration of 400 nM. Thus, the stock solution contained beads with a complex density of 1000 nM, diluted to a concentration of 400 nM. This dilution step does not change the density of the complex on the beads, only the final concentration of the complex in the stock solution.

[0164] Step 4: Tagmentation DNA samples were tagmented to generate fragments by using bead-loaded transposomes, and transposon sequences were cleaved and added to the DNA samples. In a 96-well PCR plate, 5xMg tagmentation buffer (10μL), DNA (>50ng; 10μL), dH2O (20μL), and transposome beads (prepared as in step 3; 10μL) were combined. The mixture was mixed thoroughly and incubated at 55°C for 5 minutes, followed by 20°C for 2 minutes. The tagmentation process was stopped by inactivating the transposase enzyme by treatment with SDS. 10μL of SDS was added and mixed thoroughly with the reaction mixture from the above step. The mixture was then incubated at room temperature for 5 minutes on the bench and placed on a magnetic stirrer. Once the solution became clear, the supernatant was removed.

[0165] Step 5. Stop washing tagmentation The SDS was washed off the beads to prepare the sample for PCR. The reaction mixture was removed from the magnet after tagmentation was stopped and 100 μL of wash buffer was added. The sample was vortexed at 1600 rpm for 20 seconds. It was then placed back on the magnetic stirrer and the supernatant was removed once the solution was clear. The wash step was repeated a total of three times. Once the wash was complete, all the supernatant was removed and the sample was removed from the magnetic stirrer.

[0166] Step 6. PCR Samples from step 5 were PCR amplified with primers recognizing A14 and B15 and adding the secondary adapter. The primers also contained an index sequence and a sequencing primer (P5 and P7). The master mix shown in Table 6 was added to each sample well. The beads were resuspended in the master mix and placed in a thermocycler using the program shown in Table 7. This step served to remove the untransferred / biotinylated strand, extend, and amplify to introduce P5 and P7 all in one process. [Table 6] [Table 7]

[0167] The samples were removed from the thermocycler and placed on a magnetic stirrer. 45 μL of the samples were then transferred from the PCR plate to the MIDI plate. 77 μL of water was added to the MIDI plate samples and 88 μL of Ampure SPRI beads were added to each sample / water. The mixtures were mixed thoroughly and incubated at room temperature for 5 minutes and then placed on a magnetic stirrer. Once the solution was clear, 200 μL of the samples were added to a new well on the same MIDI plate. 20 μL of Ampure SPRI beads were added and the samples were mixed thoroughly and left at room temperature for 5 minutes. They were then placed back on the magnetic stirrer.

[0168] Once the solution was clear, the supernatant was removed and discarded. The plate was placed on a magnetic stirrer and 200 μL of 80% ethanol was added without disturbing the pellet. The ethanol was later removed. The ethanol wash step was repeated a total of two more times. Once the wash was complete, any excess ethanol was removed with a pipette while the plate was on the stirrer. The samples were allowed to dry at room temperature for 5 minutes. 27 μl of water was added and mixed thoroughly. The samples were allowed to stand at room temperature for 2 minutes and placed back on the magnetic stirrer. 25 μl of the samples were transferred to a clean plate and stored at -20°C.

[0169] Example 7. A14-ME and B15-ME transposons A14-ME and B15-ME transposons were each annealed to ME' containing 3'biotin. The 3'biotin was coupled to ME' to form 3'-(I(a)) and 3'-(I(c)) linkers. The annealing reactions were in 25 μL volume using NaCl buffer. The resulting double-stranded transposons were each complexed with transposase in an overnight reaction at 37° C. After forming transposome complexes, the A14 and B15 transposome complexes were mixed together in equal volumes and loaded onto streptavidin beads at a concentration of 300 nM, resulting in complexes bound at a density of 300 nM. Once bound to the beads, the 300 nM density mixture of (I(a)) and (I(c)) was further diluted to a concentration of 120 nM. Thus, the beads still have a density of 300 nM, but the complexes are present in the diluted solution at a concentration of 120 nM. The dilution step does not change the density of the complexes on the beads, so it affects the library yield but not the insert size.

[0170] The two resulting bead-linked transposomes, 3'-(I(a)) and 3'-(I(c)), were stored at 25°C for 28 and 56 days. The Arrhenius equation estimates these to be accelerated to 4 months (28 days) and 8 months (56 days). After the accelerated time was over, the two bead-linked transposomes were taken through the tagmentation and library preparation steps as discussed above to assess the activity of the transposomes.

[0171] The bead-linked transposome complex was added to the gDNA along with a magnesium-based buffer and placed at 55°C for 5 minutes. Once complete, SDS buffer was added to the reaction and the mixture was allowed to incubate at room temperature for 5 minutes. The mixture was then placed on a magnetic stirrer and washed three times with NaCl and Tris buffer. After washing, PCR master mix and secondary adapter carriers containing index sequences were added to the beads and thoroughly resuspended. The samples were then PCR amplified to generate additional amplicons. After PCR, a SPRI cleanup was performed to remove excess carriers. The samples were run on a BioAnalyzer to measure activity (library prep yield). As shown in FIG. 6A, library yields from streptavidin bead-based solid-phase tagmentation using transposome complexes with 3'-biotinylated linkers of formula (I(a)) and (3'-(I(a)); glycerol linker) and formula (I(c)) (3'-(I(c)); hexyl linker) were compared. Linker 3'-(I(c)) provided significant library yields. Linker 3'-(I(a)) provided lower, but still sequenceable, yields. The LSC line in the figure was an arbitrary lower specification limit.

[0172] FIG. 6B illustrates accelerated stability data for sample libraries prepared from streptavidin bead-based solid-phase tagmentation using transposome complexes with a 3'-(I(a)) linker after 4 months of time effects (accelerated storage conditions at 25° C. for 28 days) compared to sample libraries prepared from a control not subjected to the time effects of the same linker for 28 days at 4° C. FIG. 6C illustrates accelerated storage data for sample libraries prepared from transposome complexes with a 3'-(I(c)) linker after 4 and 8 months of time effects (accelerated storage conditions at 25° C. for 28 and 56 days) compared to sample libraries prepared from a control not subjected to the time effects of the same linker for 28 and 56 days at 4° C., respectively.

[0173] Example 8. A14-ME and B15-ME transposons The A14-ME and B15-ME transposons were each annealed to ME' containing 3'biotin. The 3'biotin was coupled to ME' through a 3'-(I(c)) linker. The annealing reactions were in 25 μL volume using NaCl buffer. The resulting double-stranded transposons were each conjugated to transposase in an overnight reaction at 37°C. After transposome formation, the A14 and B15 transposome complexes were mixed together in equal volumes and loaded onto streptavidin beads at various densities (10 nM to 800 nM).

[0174] Various densities of bead-linked transposomes were added to gDNA with magnesium-based buffer and placed at 55°C for 5 minutes. Once complete, SDS buffer was added to the reaction and incubated at room temperature for 5 minutes. The mixture was then placed on a magnetic stirrer and washed three times with NaCl and Tris buffer. After washing, PCR master mix and secondary adapter carriers containing index sequences were added to the beads and thoroughly resuspended. PCR reactions were then performed on the samples to amplify the fragments. After PCR, SPRI size selection was performed with various SPRI ratios resulting in different insert sizes. The samples were run on a BA and on a HiSeq 2500 Rapid Output to measure activity.

[0175] Figure 7A shows the target insert size of DNA molecules as a function of bead density using streptavidin bead-based solid-phase library preparation, where the beads contain immobilized transposome complexes bound to the beads through 3'-(I(c)). Figure 7B shows the target insert size of DNA molecules as a function of SPRI conditions using streptavidin beads with immobilized transposome complexes containing hyperactive Tn5 transposase and 3'-(I(c)) linkers at a complex density of 100 nM; and Figure 7C shows the target insert size of DNA molecules as a function of SPRI conditions using streptavidin beads with immobilized transposome complexes containing hyperactive Tn5 transposase and 3'-(I(c)) linkers at a complex density of 600 nM.

[0176] Example 9. Combined Blood and Saliva Extraction Protocol Fresh whole blood was processed using the Flex Lysis Reagent kit (Illumina, Cat. No. 20015884). Fresh whole blood was collected into EDTA collection tubes and stored at 4°C before processing. Lysis master mix was prepared for each sample by mixing the following volumes: 7 μl Blood Lysis Buffer, 2 μl Proteinase K, and 31 μl Nuclease-free water. For each sample, 10 μl blood, 40 μl Lysis Master Mix, and 20 μl SPRI beads were added to one well of a 96-well PCR plate and the solution was mixed by pipetting 10 times. The plate was sealed and incubated for 10 minutes in a thermal cycler with a heated lid at 56°C. The plate was then placed on a flatbed magnet for 5 minutes, the supernatant was discarded, and 150 μl of 80% ethanol was added. After incubating on the magnet for 30 seconds, the ethanol was discarded and the plate was removed from the magnet. The beads were resuspended in 30 μl of water and were ready for library preparation.

[0177] Saliva was collected in Oragene DNA Saliva Collection tubes (DNA Genotek, Cat. No. OGR-500, OGD-510) and incubated at 50° C. for at least 1 hour to lyse the cells and then thoroughly mixed by vortexing. For each sample, 20 μl water and 30 μl saliva were added to one well of a 96-well PCR plate and mixed gently by pipetting. 20 μl SPRI beads were then added to the sample well and the beads were thoroughly mixed by pipetting the solution 10 times. The plate was incubated for 5 minutes at room temperature and then placed on a plank magnet for 5 minutes. The supernatant was removed and 150 μl of 80% ethanol was added to the bead pellet. The plate was then placed on the magnet for 30 seconds, after which the ethanol was removed and the plate was removed from the magnet. The beads were resuspended in 30 μl water and were ready for library preparation.

[0178] A number of embodiments have been described. Nevertheless, it is understood that various modifications may be made. Accordingly, other embodiments are within the scope of the following claims. For example, the present invention provides the following: (Item 1) (i) a transposase, (ii) Below: (a) a 3' portion including a first transposon end sequence; and (b) a first adapter sequence at the 5' end of the first transposon end sequence; The first transposon contains; (iii) a second transposon comprising a second transposon end sequence that is complementary to at least a portion of the first transposon end sequence; and (iv) a linker attached to the first or second transposon and comprising an affinity element; A transposome complex comprising: (Item 2) 2. The complex of claim 1, wherein the linker is attached to the second transposon at the 3' end of the second transposon. (Item 3) 3. The complex of claim 2, wherein the second end of the linker is bound to the affinity element. (Item 4) The linker and affinity element have the structure of formula (I):

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Claims

1. A transposome complex comprising: a. Transposase, b. a first transposon comprising a 3' end portion comprising a first transposon end sequence, the first transposon end sequence being linked to a first adapter sequence at the 5' end of the first transposon end sequence; c. a second transposon comprising a second transposon end sequence that is complementary to at least a portion of the first transposon end sequence; and d. a cleavable linker comprising one or more uracil nucleotides having a first end that binds to the 3' end of the second transposon and a second end that binds to an affinity element, the affinity element being capable of binding to an affinity binding partner on a solid support. A transposome complex comprising:

2. A transposome complex comprising: a. Transposase, b. a first transposon comprising a 3' end portion comprising a first transposon end sequence, the first transposon end sequence being linked to a first adapter sequence at the 5' end of the first transposon end sequence; c. a second transposon comprising a second transposon end sequence that is complementary to at least a portion of the first transposon end sequence; and d. a cleavable linker comprising one or more uracil nucleotides having a first end that binds to the 5' end of the first transposon and a second end that binds to an affinity element, the affinity element being capable of binding to an affinity binding partner on a solid support. A transposome complex comprising:

3. 3. The complex of claim 1 or 2, wherein the solid support is a tube, a well of a plate, a slide, a bead, or a flow cell.

4. The complex of claim 3 , wherein the solid support is a paramagnetic bead.

5. The complex of any one of claims 1 to 4, wherein the affinity element is biotin and the affinity binding partner is streptavidin.

6. 6. The complex of claim 1, wherein the adapter sequence comprises a universal sequence, a primer sequence, or a sequencing-related sequence, and the universal sequence comprises a region of nucleotide sequence that is complementary to a universal primer.

7. The complex according to any one of claims 1 to 6, wherein the transposase is a Tn5 transposase.

8. The complex of any one of claims 1 to 7, wherein the transposase is linked to a purification tag.

9. The complex according to any one of claims 1 to 8, wherein the first transposon end sequence and the second transposon end sequence are ME and ME', ME is AGATGTGTATAAGAGACAG (SEQ ID NO: 8) and ME' is 5'-phos-CTGTCTCTTATACATCT-3' (SEQ ID NO: 5).

10. The conjugate of any one of claims 1 to 9, wherein the cleavable linker further comprises two or more thymine residues.

11. The conjugate of any one of claims 1 to 10, wherein the cleavable linker comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 uracil nucleotides.

12. 1. A modified oligonucleotide comprising a first transposon and a second transposon, wherein the first transposon comprises a 3' end portion comprising a first transposon end sequence, the first transposon end sequence being linked to a first adapter sequence at a 5' end of the first transposon end sequence, the second transposon comprises a second transposon end sequence that is complementary to and anneals to at least a portion of the first transposon end sequence, a first end of a cleavable linker comprising one or more uracil nucleotides is attached to the 3' end of the second transposon, and a second end of the linker is attached to an affinity element, the affinity element being capable of binding to an affinity binding partner on a solid support.

13. 1. A modified oligonucleotide comprising a first transposon and a second transposon, wherein the first transposon comprises a 3' end portion comprising a first transposon end sequence, the first transposon end sequence being linked to a first adapter sequence at a 5' end of the first transposon end sequence, the second transposon comprises a second transposon end sequence that is complementary to and anneals to at least a portion of the first transposon end sequence, a first end of a cleavable linker comprising one or more uracil nucleotides is attached to the 5' end of the first transposon, and a second end of the linker is attached to an affinity element, the affinity element being capable of binding to an affinity binding partner on a solid support.

14. 12. A method of generating a library of tagged nucleic acid fragments from a double stranded target nucleic acid, comprising the steps of: fragmenting the target nucleic acid into a plurality of target fragments and incubating the target nucleic acid with a complex of any one of claims 1 to 11 under conditions sufficient to ligate the 3' end of the first transposon to the 5' end of the target fragments to generate a plurality of 5' tagged target fragments, wherein the affinity element binds to an affinity binding partner on a solid support, thereby binding the complex to the solid support.

15. The method of claim 14, wherein the affinity element is biotin and the affinity binding partner is streptavidin.

16. 1. A method for preparing a sample for sequencing, comprising: a. providing a complex according to any one of claims 1 to 11; b. applying a target nucleic acid to the complex under conditions suitable for tagmentation, thereby immobilizing fragments of the target nucleic acid to the solid support; c. amplifying the immobilized, tagmented nucleic acid; d. cleaving the cleavable site; e. enriching for the targeted amplified nucleic acid and preparing the sample for sequencing; A method comprising:

17. 17. The method of claim 16, wherein the cleaving step is accomplished by an enzyme selected from at least one of the following: a. glycosylase, or b. Apurinic / apyrimidinic (AP) endonucleases

18. 18. The method of claim 17, wherein the glycosylase is uracil DNA glycosylase, MUG, SMUG, TDG, or MBD4.

19. 19. The method of claim 18, wherein the glycosylase is uracil DNA glycosylase.

20. The AP endonuclease is Endo VIII, Endo IV, or Endo 18. The method of claim 17, wherein said compound is V.

21. The method of claim 20, wherein the AP endonuclease is Endo VIII.

22. The method of any one of claims 14 to 21, wherein the target nucleic acid is selected from at least one of the following: a. DNA b. RNA; or c. cDNA

23. 23. The method of claim 22, wherein the DNA is double stranded.

24. 24. The method of claim 23, wherein the double-stranded DNA is genomic DNA.

25. 25. The method of claim 24, wherein the genomic DNA is from a single cell, tissue, tumor, blood, plasma, urine, or cell-free nucleic acid.

26. The method of any one of claims 16 to 21, wherein the amplifying step comprises one or more of PCR or isothermal amplification.

27. 27. The method of any one of claims 14 to 26, not directly or indirectly dependent on claim 6, wherein the first or second transposon comprises a universal sequence, a primer sequence, or a sequencing related sequence, and the universal sequence comprises a region of nucleotide sequence that is complementary to a universal primer.

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