The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures, such as RCPs, in the biological sample without the use of exogenously added oligonucleotide compaction probes. In some embodiments, provided herein are methods involving the use of self-hybridizing hybridizing regions for compacting and/or stabilizing nucleic acid concatemers (e.g., RCPs). In some embodiments, dynamic inter-strand annealing between tandem units of an RCP is used for compaction and/or stabilization. In some embodiments, short palindromic regions in an RCP are used for compaction and/or stabilization.

Methods include contacting a biological sample with a first probe, where the first probe includes a capture moiety having an oligonucleotide sequence that selectively binds to a RNA in the sample, and a secondary oligonucleotide region that does not bind to the RNA, contacting the sample with a second probe, where the second probe includes a probe binding region that is complementary to, and hybridizes to, a portion of the secondary oligonucleotide region, and includes a reporter moiety, and extending the secondary oligonucleotide region using the second probe as a template to generate an extended secondary oligonucleotide region featuring multiple copies of the reporter moiety, where the reporter moiety includes a plurality of label regions each featuring an oligonucleotide sequence, and one or more of the label regions of the reporter moiety are different from the other label regions of the reporter moiety.

Methods include contacting a biological sample with a first probe, where the first probe includes a capture moiety having an oligonucleotide sequence that selectively binds to a RNA in the sample, and a secondary oligonucleotide region that does not bind to the RNA, contacting the sample with a second probe, where the second probe includes a probe binding region that is complementary to, and hybridizes to, a portion of the secondary oligonucleotide region, and includes a reporter moiety, and extending the secondary oligonucleotide region using the second probe as a template to generate an extended secondary oligonucleotide region featuring multiple copies of the reporter moiety, where the reporter moiety includes a plurality of label regions each featuring an oligonucleotide sequence, and one or more of the label regions of the reporter moiety are different from the other label regions of the reporter moiety.

Provided includes methods, compositions and systems for single molecule seeding and amplification on a flow cell. In some embodiments, nucleic acids are isothermally seeded and amplified on a flow cell comprising multiple binding areas (e.g., pads), resulting in an ensemble of substantially the same amplified molecules on each of the binding areas.

Provided includes methods, compositions and systems for single molecule seeding and amplification on a flow cell. In some embodiments, nucleic acids are isothermally seeded and amplified on a flow cell comprising multiple binding areas (e.g., pads), resulting in an ensemble of substantially the same amplified molecules on each of the binding areas.

The invention discloses a method and a system to detect a target nucleic acid sequence in a sample using padlock probe-based rolling circle amplification and nuclease protection. Padlock probe-based rolling circle amplification and nuclease protection may be used in combination with other detection assays to detect target nucleic acid sequences in a sample.

The invention discloses a method and a system to detect a target nucleic acid sequence in a sample using padlock probe-based rolling circle amplification and nuclease protection. Padlock probe-based rolling circle amplification and nuclease protection may be used in combination with other detection assays to detect target nucleic acid sequences in a sample.

Disclosed herein, inter alia, are complexes, kits, and efficient methods of sequencing two strands of a double stranded polynucleotide.

Disclosed herein, inter alia, are complexes, kits, and efficient methods of sequencing two strands of a double stranded polynucleotide.