This invention relates to the synthesis of nucleic acid-encoded chemical libraries using common adaptor sequences. Nucleic acid strands coupled to chemical moieties may be contacted with identifier oligonucleotides comprising coding sequences encoding the chemical moieties and an adaptor oligonucleotides, such that the adaptor oligonucleotide hybridizes to both the nucleic acid strands and the identifier oligonucleotides to allow ligation of the identifier oligonucleotides to the nucleic acid strands. The adaptor oligonucleotide is then removed. Nucleic acid-encoded chemical libraries, and methods of producing or screening such libraries are provided.

Provided herein is a method of reducing adapter dimer formation comprising contacting a sample comprising target nucleic acid sequences with 5 and 3 adapters in the presence of one or more hairpin oligonucleotides. Also provided is a method of preparing a library of nucleic acid sequences comprising contacting first adapter oligonucleotides with a sample comprising target nucleic acid sequences under conditions to form first ligation products, contacting the sample with one or more hairpin oligonucleotides that binds to the first adapter oligonucleotides, and contacting the sample with second adapter oligonucleotides under conditions to bind to the first ligation products and form second ligation products, wherein the second ligation products form the library of nucleic acid sequences.

Disclosed is a method for obtaining a bifunctional complex comprising a display molecule part and a coding part, wherein a nascent bifuntional complex comprising a chemical reaction site and a priming site for enzymatic addition of a tag is reacted at the chemical reaction site with one or more reactants, and provided with respective tag(s) identifying the reactant(s) at the priming site is using one or more enzymes.

Provided are methods of producing size-selected nucleic acid libraries. The methods include contacting a nucleic acid sample and a nucleic acid binding reagent including an affinity tag, under conditions in which nucleic acids of less than a desired length are substantially bound to the nucleic acid binding reagent and nucleic acids of the desired length are substantially not bound to the nucleic acid binding reagent. The conditions include the duration of the contacting, the concentration of the nucleic acid binding reagent, or both. The methods further include separating, using the affinity tag, the nucleic acids of less than the desired length bound to the nucleic acid binding reagent from the nucleic acids of the desired length not bound to the nucleic acid binding reagent, to produce a size-selected nucleic acid library. Compositions and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.

Aspects of the present disclosure relate generally to methods, compositions, and kits for preparing a ligation-based or amplicon-based library in situ, e.g., for sequencing.

Provided herein are methods and compositions relating to variant nucleic acid libraries encoding for antibodies including single domain antibodies. Libraries generated using methods described herein have improved characteristics including improved binding affinity. Libraries described herein include variegated libraries comprising nucleic acids each encoding for a predetermined variant of at least one predetermined reference nucleic acid sequence. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.

Methods and products are disclosed for asymmetrically adapting fragmented nucleic acids for next generation sequencing, including providing strand identifier sequences and index sequences to identify the source strand and sample, respectively, of the fragmented nucleic acids. The methods and products allow for efficient and reliable detection of low-frequency mutations including in subpopulations of cells within a subject and also for the amplification of the fragmented nucleic acids when there is a low yield of isolated fragmented nucleic acids.

The present invention refers to a method for the separation/identification of reagents comprising a compound library, such as DNA-encoded Libraries (DELs), which enter target cells or localize to a desired subcellular compartment of said target cells, by amplifying and modifying the signal of a barcode attached to said reagents thereby significantly increasing the signal to noise ratio and distinguishing the reagents that successfully entered the desired cells or the desired subcellular compartment. Further disclosed herein are reagents, said reagent being able to enter a desired subcellular compartment of a target cell as well as therapeutic applications of said reagents.

Provided herein is a method of identifying modified cytosines in genomic DNA in a biological sample. The method includes isolating, from the biological sample, nucleic acids comprising genomic DNA comprising cytosines and modified cytosines, contacting the isolated genomic DNA under conditions resulting in deamination of the genomic DNA thereby converting at least some of the cytosines in the genomic DNA to uracil and at least some of the modified cytosines to thymine, contacting the deaminated, isolated the genomic DNA with an enzyme to remove uracil from the genomic DNA, amplifying the genomic DNA lacking uracil using primary-directed template amplification, and sequencing the genomic DNA, wherein the sequencing identifies the modified cytosines in the genomic DNA of the single cell.

An object of the present invention is to provide a method capable of more easily screening for, with higher accuracy, a sequence that regulates display efficiency in a polynucleotide display method. The problem is solved by a method for screening for a sequence that regulates display efficiency in a polynucleotide display method, the screening method including steps of: (a) binding a polynucleotide-polypeptide complex, which is obtained through translation by a cell-free translation system from a polynucleotide including a polypeptide encoding sequence and random sequences, to a solid phase via a modification substance on the polypeptide in the polynucleotide-polypeptide complex; and (b) selecting a random sequence by using, as an index, a ratio (enrichment factor) of appearance frequency of each random sequence in the polynucleotide-polypeptide complex bound to the solid phase with respect to appearance frequency of each random sequence in the polynucleotide.