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.

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.

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 disclosure relates to engineered systems and methods for detecting target nucleic acid in a sample, which may be a complex mixture. The systems and methods may improve sensitivity of target nucleic acid detection by enhancing signal generation. For example, signal generation may be enhanced through programmable capture and concentration of the target nucleic acid using an engineered type III CRISPR complex. Various ancillary nucleases such as Can1, Can2, and NucC are identified and may be used for detection. For example, binding of the engineered type III CRISPR complex may produce products that activate the identified ancillary nucleases. Different activators trigger changes in the substrate specificity of these nucleases. The activated nucleases may be used to detect programmatic detection of the target nucleic in the sample. The systems and methods are shown to detect viral RNA directly from nasopharyngeal swab samples.

The disclosure relates to engineered systems and methods for detecting target nucleic acid in a sample, which may be a complex mixture. The systems and methods may improve sensitivity of target nucleic acid detection by enhancing signal generation. For example, signal generation may be enhanced through programmable capture and concentration of the target nucleic acid using an engineered type III CRISPR complex. Various ancillary nucleases such as Can1, Can2, and NucC are identified and may be used for detection. For example, binding of the engineered type III CRISPR complex may produce products that activate the identified ancillary nucleases. Different activators trigger changes in the substrate specificity of these nucleases. The activated nucleases may be used to detect programmatic detection of the target nucleic in the sample. The systems and methods are shown to detect viral RNA directly from nasopharyngeal swab samples.

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.

The present invention relates to a digital multiplex method for detecting and/or quantifying multiple target biomolecules in a sample, said biomolecules being selected from DNA, RNA, and proteins. The present invention further relates to different applications of the digital multiplex method and to a kit.

The present invention relates to a digital multiplex method for detecting and/or quantifying multiple target biomolecules in a sample, said biomolecules being selected from DNA, RNA, and proteins. The present invention further relates to different applications of the digital multiplex method and to a kit.