The present invention provides, among other things, methods of quantitating mRNA capping efficiency, particularly for mRNA synthesized in vitro. In some embodiments, the methods comprise chromatographic methods of quantifying capping efficiency and methylation status of the caps.

A method for investigating intra- and/or intermolecular interactions involving RNA is provided. The method includes a) synthesizing a RNA/DNA heteroduplex (RDH) comprising a RNA strand of interest paired to a DNA strand; b) binding a first end of the DNA strand and a corresponding first end of the RNA strand to a first element of a nanoscale manipulating device, and a second end of the DNA strand to a second element of the nanoscale manipulating device, leaving a second end of the RNA strand free; c) moving the first and second elements of the manipulating device apart from each other, stretching the DNA strand and causing the RNA strand to peel off the heteroduplex; and d) moving the first and second elements of the nanoscale manipulating device towards each other, allowing the DNA strand to relax and causing the RNA strand to bind again to it. Measurement of a force-displacement relationship during steps c) and d) provides information on intra- and/or intermolecular interactions involving the RNA strand. Also provided is an apparatus for carrying out the method.

A method for investigating intra- and/or intermolecular interactions involving RNA is provided. The method includes a) synthesizing a RNA/DNA heteroduplex (RDH) comprising a RNA strand of interest paired to a DNA strand; b) binding a first end of the DNA strand and a corresponding first end of the RNA strand to a first element of a nanoscale manipulating device, and a second end of the DNA strand to a second element of the nanoscale manipulating device, leaving a second end of the RNA strand free; c) moving the first and second elements of the manipulating device apart from each other, stretching the DNA strand and causing the RNA strand to peel off the heteroduplex; and d) moving the first and second elements of the nanoscale manipulating device towards each other, allowing the DNA strand to relax and causing the RNA strand to bind again to it. Measurement of a force-displacement relationship during steps c) and d) provides information on intra- and/or intermolecular interactions involving the RNA strand. Also provided is an apparatus for carrying out the method.

The present disclosure provides methods for preparing a target mutant nucleic acid for subsequent enrichment relative to a wild type nucleic acid using nucleases that have a substantially higher activity on double stranded DNA versus single stranded DNA or RNA. The present disclosure also includes methods for enriching a target mutant nucleic acid and for preparing unmethylated/methylated nucleic acids of interest for subsequent enrichment.

The present disclosure provides methods for preparing a target mutant nucleic acid for subsequent enrichment relative to a wild type nucleic acid using nucleases that have a substantially higher activity on double stranded DNA versus single stranded DNA or RNA. The present disclosure also includes methods for enriching a target mutant nucleic acid and for preparing unmethylated/methylated nucleic acids of interest for subsequent enrichment.

The present disclosure provides a system and method for depleting target nucleic acids from a nucleic acid sample. In one aspect, a kit according to the present disclosure includes a plurality of DNA probes. Each of the DNA probes is hybridizable to form a heteroduplex with at least one of a plurality of target RNA transcripts in a nucleic acid sample. The number of unique target RNA transcripts hybridized by the plurality of DNA probes is at least three. The kit further includes an enzyme having RNA-DNA hybrid ribonucleotidohydrolase activity, where degrades at least the RNA portion of the heteroduplex.

The present disclosure provides a system and method for depleting target nucleic acids from a nucleic acid sample. In one aspect, a kit according to the present disclosure includes a plurality of DNA probes. Each of the DNA probes is hybridizable to form a heteroduplex with at least one of a plurality of target RNA transcripts in a nucleic acid sample. The number of unique target RNA transcripts hybridized by the plurality of DNA probes is at least three. The kit further includes an enzyme having RNA-DNA hybrid ribonucleotidohydrolase activity, where degrades at least the RNA portion of the heteroduplex.

Provided herein are methods, compositions, and kits for generating a nucleic acid library. In various embodiments provided herein, transposomes comprising transposases are used in forming dual-end tagged nucleic acid molecules for downstream amplification and nucleic acid molecule processing steps.

Provided herein are methods, compositions, and kits for generating a nucleic acid library. In various embodiments provided herein, transposomes comprising transposases are used in forming dual-end tagged nucleic acid molecules for downstream amplification and nucleic acid molecule processing steps.

Methods, systems, kits and compositions are described for quality control and quantitation of nucleic acid libraries of double stranded nucleic acid libraries prior to massively parallel sequencing. Electrophoretic separation within a channel using a detectably labeled single stranded sizing ladder may be used to define the molecular weight range and amount of the double stranded nucleic acids.