Described herein are RNA arrays, and compositions and methods for generating RNA arrays, particularly high density RNA arrays. The disclosed methods for generating RNA arrays utilize template DNA arrays and RNA polymerase to generate RNA arrays. In some embodiments, the disclosed methods use an RNA polymerase and modified ribonucleosides to generate modified RNA arrays for various applications, e.g. RNA arrays having higher nuclease resistance, more conformationally stable RNA arrays, and higher binding affinity RNA aptamer arrays. In some embodiments, the disclosed methods are used to generate RNA bead arrays.

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.

An article including: a substrate; and at least one immobilization site on the substrate comprising at least one nucleic acid immobilization site, each site having a first layer of a tie agent in contact with the substrate, and a second layer of a dendrimer mobilizing agent in contact with the first layer. Also disclosed is a method of making and a method of using the article.

The invention is directed to methods for synthesizing oligonucleotides direction on biomolecules or cells living or fixed. In some embodiments, template-free enzymatic synthesis is implemented under biological conditions with successive cycles of (i) enzymatic addition of a 3′-O-blocked nucleoside triphosphate and (ii) enzymatic deblocking of the incorporated nucleotide to regenerate a free 3′ hydroxyl. The invention has applications in single-cell cDNA library construction and analysis.

According to one embodiment of the present invention, a structure includes: a substrate having a patterned surface of one or more binding sites; and a molecular shape made by a polynucleotide platform having a shape corresponding to a shape of a binding site of the one or more binding sites, the molecular shape being bound to one of the one or more binding sites.

Disclosed are methods for preparing a DNA library directly from a stool sample. The method comprises applying the stool sample directly to a buffer, heating and cooling the buffer, separating a supernatant within the buffer from a precipitate using centrifugation, and transferring the supernatant into a first reaction vessel containing a first reagent mixture to yield a first reaction mixture. The method also comprises subjecting the first reaction mixture to a first PCR protocol, purifying amplicons within the first reaction vessel through a first purification procedure to yield a purified target amplicon solution, transferring the purified target amplicon solution to a second reaction vessel comprising a second reagent mixture to yield a second reaction mixture, and subjecting the second reaction mixture to a second PCR protocol. The method further comprises purifying index-tagged amplicons within the second reaction vessel through a second purification procedure to yield the DNA library.

Disclosed are methods for preparing a DNA library directly from a stool sample. The method comprises applying the stool sample directly to a buffer, heating and cooling the buffer, separating a supernatant within the buffer from a precipitate using centrifugation, and transferring the supernatant into a first reaction vessel containing a first reagent mixture to yield a first reaction mixture. The method also comprises subjecting the first reaction mixture to a first PCR protocol, purifying amplicons within the first reaction vessel through a first purification procedure to yield a purified target amplicon solution, transferring the purified target amplicon solution to a second reaction vessel comprising a second reagent mixture to yield a second reaction mixture, and subjecting the second reaction mixture to a second PCR protocol. The method further comprises purifying index-tagged amplicons within the second reaction vessel through a second purification procedure to yield the DNA library.

Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5′-tagged double-stranded target DNA on a surface. The methods are useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.

Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5′-tagged double-stranded target DNA on a surface. The methods are useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.

A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.