Disclosed are methods for performing aptamer preselection based on unique geometry and the content of stems or loops of the aptamer, which methods are capable of providing suitable binders and also permit selection of aptamers performed essentially entirely on a chip or other device. Also disclosed are kits for aptamer selection.

A method having steps of (a) providing nucleic acids having a tag sequence (N.sub.1).sub.n(N.sub.2).sub.n . . . (N.sub.x).sub.n, wherein N.sub.1, N.sub.2 and N.sub.x are nucleotides that complement different nucleotides, respectively, wherein n is an integer that can differ for N.sub.1, N.sub.2 and N.sub.x; (b) detecting the nucleic acids individually and under conditions to distinguish signal intensities for (N.sub.1).sub.n sequences having different values for n, (N.sub.2).sub.n sequences having different values for n and. (N.sub.x).sub.n sequences having different values for n; and (c) distinguishing the tags based on the signal intensities.

A method having steps of (a) providing nucleic acids having a tag sequence (N.sub.1).sub.n(N.sub.2).sub.n . . . (N.sub.x).sub.n, wherein N.sub.1, N.sub.2 and N.sub.x are nucleotides that complement different nucleotides, respectively, wherein n is an integer that can differ for N.sub.1, N.sub.2 and N.sub.x; (b) detecting the nucleic acids individually and under conditions to distinguish signal intensities for (N.sub.1).sub.n sequences having different values for n, (N.sub.2).sub.n sequences having different values for n and. (N.sub.x).sub.n sequences having different values for n; and (c) distinguishing the tags based on the signal intensities.

The present disclosure is directed to methods and kits for identifying, enriching, and evaluating templated assembly reactants. Some embodiments disclose methods for identifying templated assembly targets by synthesizing templated assembly reactants, hybridizing the templated assembly reactants to target nucleic acids, performing a templated assembly reaction, and identifying the target nucleic acids that hybridized to the templated assembly reactants. Libraries of templated assembly reactants, a kit for identifying templated assembly targets, and a pair of templated assembly targets enriched from a library of chemically-ligated oligonucleotides spatially elicited (CLOSE) products are also disclosed.

Provided herein are polypeptides that bind to a transferrin receptor, methods of generating such polypeptides, and methods of using the polypeptides to target a composition to a transferrin receptor-expressing cell.

Provided herein are polypeptides that bind to a transferrin receptor, methods of generating such polypeptides, and methods of using the polypeptides to target a composition to a transferrin receptor-expressing cell.

Provided are methods for detecting and analyzing polynucleotides in a biological sample or sample derived therefrom for example, using a synthetic template polynucleotide. In some aspects, a target polynucleotide in the sample hybridizes to the template polynucleotide and is extended by a polymerase, generating an extended target polynucleotide. In some examples, the extended target polynucleotide is amplified, for example, by polymerase chain reaction, and sequences of the target polynucleotide determined, for example, by priming in the region of the extended target polynucleotide generated by extension and sequencing towards the region having identity to the target polynucleotide. In some aspects, the target polynucleotide is thereby detected in the sample and its sequence identified. In some aspects, the provided methods can be used to capture polynucleotide fragments in a biological sample, for example, plasma, and determine respective biomarkers they carry, for example, for cancer diagnosis and prognosis.

Improved methods to quantitate RNA in biological or other analytical samples employ extended RNAs containing adaptors at the 5 end and polyA sequences coupled to a tag at the 3 end. The invention method is particularly useful in quantitating microRNAs as primers can be used that need not complement the non-conserved 3 ends of these molecules.

Improved methods to quantitate RNA in biological or other analytical samples employ extended RNAs containing adaptors at the 5 end and polyA sequences coupled to a tag at the 3 end. The invention method is particularly useful in quantitating microRNAs as primers can be used that need not complement the non-conserved 3 ends of these molecules.

Provided herein are high-throughput sequencing methods to study the diversity and functionality of lymphocyte receptor chains and pairing of the same. Specifically, the methods provided herein are used to identify with confidence one or more lymphocyte receptor chain pairs in a sample, for example one or more functional chain pairs.