This present disclosure describes hybridization probes modularly constructed from several oligonucleotides with a pattern of designed complementary interactions, allowing the probes to sequence-specifically capture or analyze nucleic acid target sequences that are long and/or complex.

Methods for RNA detection in biological samples include (a) contacting a biological sample with a first composition featuring multiple different types of unlabeled oligonucleotide probes that hybridize to RNA species in the sample; (b) contacting the biological sample with a hybridization agent featuring a chaotropic compound; (c) contacting the biological sample with a second composition that includes multiple different types of labeled oligonucleotide probes, where each of the different types of labeled oligonucleotide probes selectively hybridizes to one of the different types of unlabeled oligonucleotide probes; (d) obtaining at least one image of the biological sample with the multiple different types of labeled oligonucleotide probes bound to the sample; and (e) identifying spatial locations of the RNA species in the sample based on components of the at least one image that correspond to the different types of labeled oligonucleotide probes, where the biological sample is contacted with the second composition under isothermal conditions.

Methods for RNA detection in biological samples include (a) contacting a biological sample with a first composition featuring multiple different types of unlabeled oligonucleotide probes that hybridize to RNA species in the sample; (b) contacting the biological sample with a hybridization agent featuring a chaotropic compound; (c) contacting the biological sample with a second composition that includes multiple different types of labeled oligonucleotide probes, where each of the different types of labeled oligonucleotide probes selectively hybridizes to one of the different types of unlabeled oligonucleotide probes; (d) obtaining at least one image of the biological sample with the multiple different types of labeled oligonucleotide probes bound to the sample; and (e) identifying spatial locations of the RNA species in the sample based on components of the at least one image that correspond to the different types of labeled oligonucleotide probes, where the biological sample is contacted with the second composition under isothermal conditions.

Provided is a method for multiplex and asymmetric amplification of one or more target nucleic acids in a sample. The method can simultaneously amplify multiple target nucleic acids existing in a sample, and can simultaneously produce a large number of single-chain products.

Provided is a method for multiplex and asymmetric amplification of one or more target nucleic acids in a sample. The method can simultaneously amplify multiple target nucleic acids existing in a sample, and can simultaneously produce a large number of single-chain products.

The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Provided herein are methods and compositions for creating a sequencing library comprising a target nucleic acid. Methods herein can comprise: contacting a nucleic acid sample to a first population of primers, a polymerase, dNTPs, and labeled ddNTPs; performing an extension reaction thereby creating an labeled extension product; contacting the extension product to a second population of primers to create a double stranded extension product comprising the target nucleic acid; contacting the double stranded extension product to a target specific enzyme under conditions allowing cleavage of at least a subset of the double stranded extension product thereby creating a cleaved target nucleic acid; and isolating the cleaved target nucleic acid.

Provided herein are methods and compositions for creating a sequencing library comprising a target nucleic acid. Methods herein can comprise: contacting a nucleic acid sample to a first population of primers, a polymerase, dNTPs, and labeled ddNTPs; performing an extension reaction thereby creating an labeled extension product; contacting the extension product to a second population of primers to create a double stranded extension product comprising the target nucleic acid; contacting the double stranded extension product to a target specific enzyme under conditions allowing cleavage of at least a subset of the double stranded extension product thereby creating a cleaved target nucleic acid; and isolating the cleaved target nucleic acid.

Provided herein are methods of determining a surgical margin and the site and size of a tissue to be resected from a subject, and methods of use thereof.