20results about "Library linkers" patented technology

Provided herein are compositions and methods for normalizing sequencing libraries. Further provided herein are adapter conjugates and hybrid circular adapters, composition comprising the same, and methods of generating the same. Further provided herein are methods of using the adapter conjugates, hybrid circular adapters, and compositions comprising the same to normalize genomic DNA libraries for next-generation sequencing.

Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.

The present invention provides a method for constructing a cyclic compound library that overcomes the limitations of conventional ring-closing methods for cyclic compound libraries, has the advantages of milder ring-closing reaction conditions and high generality, can be used to construct monocyclic and bicyclic compound libraries, and involves few side reactions. [Solution] A cyclic compound library and its construction method are provided, which uses a solid support, a molecule containing a photocleavable group, a linker, a building block, a ring-closing A-terminal molecule, and a ring-closing B-terminal molecule at both ends of the reaction synthesis, and utilizes the decomposition of the solid support under light irradiation to complete ring closure of the amino acid residue structures of the ring-closing A-terminal molecule A and the ring-closing B-terminal molecule B through the action of cyclohydrolase. This method, which uses mild ring closure conditions, is more universal and expands the types of chemical reactions and the diversity of the encoded compound library.

A method for DNA synthesis using protected nucleosides is disclosed. The nucleosides may be nucleoside triphosphates or nucleoside phosphoramidites with nucleobases attached to electrochemically-cleavable linkers. Removal of a protecting group by application of a voltage in solution triggers a cyclization reaction that cleaves the electrochemically-cleavable linkers. The electrochemically-cleavable linkers may include an amide linkage and an amide that forms a lactam or an ester linkage and a protected alcohol that forms a lactone when the protecting group is removed. The voltage used to cleave the electrochemically-cleavable linkers may be generated by activation of individual electrodes on a microelectrode array. The microelectrode array can be a substrate for solid-phase synthesis of oligonucleotides. Activation of specific electrodes removes the protecting groups at those electrodes and thus enables spatially-controlled extension of the oligonucleotides. Protected nucleosides linked to protecting groups by electrochemically-cleavable linkers are also disclosed.

Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.

Provided is a 5'-ligation-based single-stranded DNA-specific high-throughput sequencing method, relating to the technical field of biology. The present invention specifically comprises a method for preparing a 5'-end-ligation-based single-stranded DNA sequencing library. The method comprises the following steps of treating a sample to be detected: step 1) using a DNA polymerase without exonuclease activity to fill in the 5' end of dsDNA; step 2) adding a tail to the 3' end; (3) ligating a 5' stem loop adapter having undergone renaturation treatment, wherein the structure of the 5' stem loop adapter is an overhang-a random base region-a first stem region-a loop region-a second stem region, and the first stem region and the second stem region form a double strand by means of renaturation; and step 4) carrying out amplification on a ligated product. The amplified product constitutes a single-stranded DNA sequencing library.

The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by blocking the 3′ ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing, by exonuclease treatment and optionally blocking the 3′ ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing, by exonuclease treatment after protective adapters are ligated to target polynucleotides to degrade unincorporated adapters prior to amplification and sequencing, and / or by modifying or blocking 5′ and 3′ ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.

Provided herein are compositions and methods to identify a binding element (e.g., peptide, peptoid, or protein) that can be bound by an immunoreceptor (e.g., antibody). The binding element can be provided in a target binding unit comprising two binding elements separated by a spacer such that the two binding elements simultaneously bind to a single molecule comprising an antigen binding domain of an antibody. The present disclosure provides various strategies to construct the spacer. The identified binding elements can be further used to manufacture an array which can be used to profile antibodies obtained from a blood sample.

A method for preparing a 5′-end ligation-based ssDNA-specific sequencing (Liss-seq) library is provided. The method includes: (a) treating a DNA sample to be tested that includes single-stranded DNA and double-stranded DNA with Klenow Fragment (3′→5′exo−) DNA polymerase to fill in 5′ ends of the double-stranded DNA to obtain a first reaction product; (b) conducting a 3′ end tail addition reaction on the first reaction product to obtain a second reaction product; (c) ligating the second reaction product with a renatured 5′ hairpin adaptor to obtain a ligation product; a structure of 5′ hairpin adaptor being: 5′-overhang-random base region-first stem region-loop region-second stem region-3′, the first stem region and the second stem region forming a double-strand through a renaturation treatment; and (d) amplifying the ligation product to obtain the Liss-seq library, a length of the overhang being within a range of 0-20 nt.

Provided herein are engineered terminal deoxynucleotidyl transferase (TdT) proteins with certain modifications, including mutations to confer thermal stability and to install an exposed amino acid residue to which a small molecule can be covalently tethered via bioconjugate chemistries such as click chemistry. Also provided herein are methods of nucleic acid molecule synthesis using engineered TdTs and nucleotide molecules attached to redox-cleavable linkers, wherein the engineered TdT incorporates the nucleotide molecule into a nucleic acid strand and is separated from the nucleotide molecule when the redoxcleavable linker is cleaved upon exposure to suitable electrochemical conditions. Also provided herein are engineered TdTs covalently attached to a nucleotide molecule via a tether and also nucleotide molecules comprising a redox-cleavable linker. Further provided herein are systems for enzymatic DNA synthesis comprising an engineered TdT, a redox-cleavable linker a redox shuttle solution, and two or more electrodes.

The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by modifying or blocking 5′ and 3′ ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.

The present invention provides a method for constructing a cyclic compound library that overcomes the limitations of conventional ring-closing methods for cyclic compound libraries, has the advantages of milder ring-closing reaction conditions and high generality, can be used to construct monocyclic and bicyclic compound libraries, and involves few side reactions. [Solution] A cyclic compound library and its construction method are provided, which uses a solid support, a molecule containing a photocleavable group, a linker, a building block, a ring-closing A-terminal molecule, and a ring-closing B-terminal molecule at both ends of the reaction synthesis, and utilizes the decomposition of the solid support under light irradiation to complete ring closure of the amino acid residue structures of the ring-closing A-terminal molecule A and the ring-closing B-terminal molecule B through the action of cyclohydrolase. This method, which uses mild ring closure conditions, is more universal and expands the types of chemical reactions and the diversity of the encoded compound library.

Provided is a 5'-end ligation-based single-stranded DNA (ssDNA)-specific high-throughput sequencing method, relating to the technical field of biology. The present disclosure specifically comprises a method for preparing a 5'-end ligation-based ssDNA-specific sequencing (Liss-seq) library. The method comprises the following steps of treating a sample to be tested: 1) using a DNA polymerase without exonuclease activity to fill in 5' ends of double-stranded DNA (dsDNA); 2) adding a tail to the 3' end; (3) ligating a renatured 5' hairpin adaptor; a structure of the 5' hairpin adaptor being: overhang-random base region-first stem region-loop region-second stem region, and the first stem region and the second stem region forming a double strand by means of renaturation; and 4) carrying out amplification on a ligated product. The amplified product constitutes a ssDNA sequencing library.

Provided herein are compositions and methods for normalizing sequencing libraries.Further provided herein are adapter conjugates and hybrid circular adapters, compositions comprising them, and methods for producing them.Further provided herein are methods for normalizing genomic DNA libraries for next-generation sequencing using adapter conjugates, hybrid circular adapters, and compositions comprising them.

A method for preparing a 5′-end ligation-based ssDNA-specific sequencing (Liss-seq) library is provided. The method includes: (a) treating a DNA sample to be tested that includes single-stranded DNA and double-stranded DNA with Klenow Fragment (3′→5′exo−) DNA polymerase to fill in 5′ ends of the double-stranded DNA to obtain a first reaction product; (b) conducting a 3′ end tail addition reaction on the first reaction product to obtain a second reaction product; (c) ligating the second reaction product with a renatured 5′ hairpin adaptor to obtain a ligation product; a structure of 5′ hairpin adaptor being: 5′-overhang-random base region-first stem region-loop region-second stem region-3′, the first stem region and the second stem region forming a double-strand through a renaturation treatment; and (d) amplifying the ligation product to obtain the Liss-seq library, a length of the overhang being within a range of 0-20 nt.

Systems, methods, and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions on the biomolecules. Some embodiments include preparation of nucleic acid reactions within the bead, wherein the bead includes pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest.

The present disclosure provides compositions and methods for identifying binding elements (e.g., peptides, peptoids, or proteins) that can be bound by an immune receptor (e.g., an antibody). The binding element can be provided in a target binding unit that includes two binding elements separated by a spacer such that the two binding elements simultaneously bind to a single molecule that includes an antigen-binding domain of an antibody. The present disclosure provides various strategies for constructing the spacer. The identified binding elements can also be used to fabricate arrays that can be used to profile antibodies obtained from a blood sample.

The present disclosure provides, in part, electrochemical sensors and aptamers for detecting phenol-soluble modulins (PSMs) and methods of preparing and using the same, e.g., for detecting Staphylococcus spp.

To provide modulation of polymer beads for DNA processing.SOLUTION: Systems, methods and compositions provided herein relate to preparation of beads encapsulating biomolecules for performing sequential reactions of the biomolecules. Some embodiments include preparation of nucleic acid reactions within the beads, where the beads include pores that allow diffusion of molecules into or out of the beads while retaining other molecules of interest. In some embodiments, the bead is a porous hydrogel bead or a porous hollow bead. In some embodiments, the bead comprises multiple polymer layers, where each layer has a distinct pore size and pore density. In some embodiments, the pores are modulated in a size on the basis of changes in a charge, a pH, or a temperature.SELECTED DRAWING: None

Provided herein are compositions and methods for standardizing a sequencing library. Also provided herein are adapter conjugates and hybridized cyclic adapters, compositions comprising the same, and methods of producing the same. Also provided herein are methods of standardizing genomic DNA libraries for next generation sequencing using the adapter conjugates, hybrid circular adapters, and compositions comprising them.