Methods of amplifying libraries after introduction of dihydrouracil (DHU) residues by methods such as TET-assisted Pyridine Borane Sequencing (TAPS), and variants of TAPS including TAPS with blocking by -glucosylation (TAPS) and Chemically-assisted Pyridine Borane Sequencing (CAPS) are described. The methods comprise introducing DHU residues into a nucleic acid sample and preparation of a sequencing library by a complementary strand synthesis step reaction with a first polymerase or polymerase mixture that is tolerant of DHU residues and/or products resulting from the introduction of the DHU residues and/or the TAPS process followed by exponential amplification. Improved methods for conversion of oxidized nucleotide residues to DHU are also described.

Provided is a method for replicating a mirror nucleic acid, comprising: reacting a mirror nucleic acid template, a mirror nucleic acid primer and mirror dNTPs/rNTPs in the presence of a mirror nucleic acid polymerase, so as to obtain the mirror nucleic acid.

The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.

Methods determine corrected image data acquired by a nucleic acid sequencer during a cycle. Such methods may: (a) obtain an image of a substrate including a plurality of sites where nucleic acid bases are read; (b) measure color values of the plurality of sites from the image of the substrate; (c) store the color values in a processor buffer; (d) retrieve partially phase-corrected color values of the plurality of sites, where the partially phase-corrected color values were stored in the sequencer's memory during an immediately preceding base calling cycle; (e) determine a prephasing correction; and (f) determine the corrected color values. In implementations, these operations are all performed during a single base calling cycle. In embodiments, the methods additionally include using the corrected color values to make base calls for the plurality of sites.

Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template ribonucleic acid (RNA), a template switch oligonucleotide including a 3 hybridization domain and a sequencing platform adapter construct, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template RNA and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid that includes a region polymerized from the dNTPs by the polymerase. Aspects of the invention further include compositions and kits.

The present invention relates to particles comprising a magnetic core coated in a polymeric gel, methods of making such particles, and methods of using such particles, for example to support both chemical and biological synthesis.

Disclosed is a method and compounds useful for performing said method for simultaneous synthesis of a plurality of oligonucleotide molecules, and more specifically for orthogonal synthesis of at least two different oligonucleotide molecules at the same time with applications in combinatorial chemistry and DNA encoded libraries (DEL).

The present invention relates to a method for the generation of a cDNA library from transfer RNA (tRNA) comprising (a) optionally ligating at least one DNA adapter to 3-end of tRNA, wherein 3-end of the DNA adapter is preferably a chain terminator dideoxycytidine, preferably under one or more of the following conditions: (i) crowding reagent at 5% to 35%, preferably 15% to 30%, and most preferably about 25%, (ii) MgCl.sub.2 concentration of 1 mM to 15 mM, preferably 3 to 12 mM and most preferably about 10 mM (iii) a temperature of 12 C. to 37 C., preferably of about 25 C. (iv) a pH of 6.0 to 9.0, preferably 6.5 to 8.0 and most preferably about 7.0, (v) reducing agent concentration of 0.1 mM to 10 mM, preferably 0.5 to 5 mM and most preferably about 1 mM, and (vi) a reaction time of at least 30 min, preferably at least 1.5 h and most preferably at least 3 h; and (b) reverse transcription in a primer-dependent reaction, in case step (a) is present, or in a template-switching reaction, in case step (a) is absent, of tRNAs into cDNA by a group II intron reverse transcriptase, under the following conditions: (i) KCl or NaCl at a concentration of 20 mM to 250 mM, preferably 50 to 100 mM and most preferably about 75 mM, (ii) MgCl.sub.2 at a concentration of 0.5 mM to 15 mM, preferably 1 to 5 mM and most preferably about 3 mM, (iii) a temperature of 30 C. to 65 C., preferably of about 42 C., and (iv) a reaction time of at least 2 h, preferably at least 8 h and most preferably at least 15 h, and preferably (v) a pH of 6.5 to 9.5, preferably 7.0 to 8.5 and most preferably about 8.0, and/or (vi) a reducing agent (DTT) at a concentration of 1 mM to 12.5 mM, preferably 3 to 8 mM and most preferably about 5 mM.

Provided is a method of preparing at least one ligation product from a sample including a plurality of single-strand nucleic acid fragments, the method including the steps of: (a) ligating a first universal oligonucleotide adaptor to at least one single-strand nucleic acid fragment, wherein the first universal oligonucleotide adaptor is configured for ligating to a 3 end of individual single-strand nucleic acid fragment; and (b) ligating a second universal oligonucleotide adaptor to the at least one single-strand nucleic acid fragment, wherein the second universal oligonucleotide adaptor is configured for ligating to a 5 end of individual single-strand nucleic acid fragment, thereby at least one ligation product is formed. In another embodiment, provided is at least one cancer biomarker comprising human telomere sequence with two or more consecutive repeats of nucleotide sequence TTAGGG.

Provided herein are methods for generating circular nucleic acid molecules and circular nucleic acid libraries. The methods can be used to generate clonal populations of target nucleic acid molecules for downstream applications such as sequencing.