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.

Phosphoramidate-based monomers are provided for use in the synthesis of expandable polymers for nanopore-based sensing. Such monomers comprising a reporter construct that contain a first reporter code, a symmetrical chemical brancher bearing a translocation control element, and a second reporter code, wherein the ends of the reporter construct are attached to phosphoramidate-nucleoside. Related methods and products are also provided.

Phosphoramidate-based monomers are provided for use in the synthesis of expandable polymers for nanopore-based sensing. Such monomers comprising a reporter construct that contain a first reporter code, a symmetrical chemical brancher bearing a translocation control element, and a second reporter code, wherein the ends of the reporter construct are attached to phosphoramidate-nucleoside. Related methods and products are also provided.

A method for specifically and efficiently quantifying the expression of targeted RNA variants with specific terminal sequences suitable to identify multiple isoforms bearing complex heterogeneity in terminal sequences by hybridizing a 5′-Dbs-adapter to the 5′-end of target RNAs, wherein the 5′-Dbs-adapter has a stem-loop structure whose protruding 5′-end base-pairs with the 5′-end of target RNAs, and wherein the loop region of 5′-Dbs-adapter contains a base-lacking spacer which will terminate reverse transcription in a subsequent step; hybridizing a 3′Db-adapter to the 3′-end of target RNAs, wherein the 3′-Db-adapter has a stem-loop structure whose protruding 3′-end base-pairs with the 3′-end of target RNAs; ligating both adapters with target RNAs by RN12 ligation to form a “dumbbell-like” structure; and, amplifying and quantifying the ligation product by RT-PCR.

The invention is directed to a method to obtain the spatial location and sequence information of a target sequence in a sample comprising at least one m-RNA strand comprising the steps a. providing a surface with a plurality of spacer units capable of binding at least one m-RNA strand and with at least one fiducial marker b. providing a sample comprising at least one m-RNA strand to the surface wherein at least one m-RNA strand of the sample binds to at least one spacer unit creating at least one single stranded oligomer c. taking a first image of the surface to obtain the spatial information of the sample relative to the fiducial marker d. removing sample form surface e. hybridizing at least one oligonucleotide comprising 50-1000 nucleic acids with its 5′ and 3′ ends to complementary parts of the single stranded oligomer thereby forming a padlock-shaped structure that is ligated to create a single strand circular template f. multiplying the single strand circular template by a polymerase capable of rolling circle amplification into a plurality of DNA concatemers thereby forming rolonies g. obtaining the sequence information of the rolonies h. linking the spatial information of the sample with the sequence information of the rolonies.

The invention is directed to a method to obtain the spatial location and sequence information of a target sequence in a sample comprising at least one m-RNA strand comprising the steps a. providing a surface with a plurality of spacer units capable of binding at least one m-RNA strand and with at least one fiducial marker b. providing a sample comprising at least one m-RNA strand to the surface wherein at least one m-RNA strand of the sample binds to at least one spacer unit creating at least one single stranded oligomer c. taking a first image of the surface to obtain the spatial information of the sample relative to the fiducial marker d. removing sample form surface e. hybridizing at least one oligonucleotide comprising 50-1000 nucleic acids with its 5′ and 3′ ends to complementary parts of the single stranded oligomer thereby forming a padlock-shaped structure that is ligated to create a single strand circular template f. multiplying the single strand circular template by a polymerase capable of rolling circle amplification into a plurality of DNA concatemers thereby forming rolonies g. obtaining the sequence information of the rolonies h. linking the spatial information of the sample with the sequence information of the rolonies.

Disclosed herein are compositions for detecting the presence of one or more target(s) of interest, wherein the composition comprises a first hairpin initiator molecule and a second initiator molecule. Also disclosed herein are methods of using the same.

Disclosed herein are compositions for detecting the presence of one or more target(s) of interest, wherein the composition comprises a first hairpin initiator molecule and a second initiator molecule. Also disclosed herein are methods of using the same.

The present invention provides an oligonucleotide probe for single nucleotide polymorphism detection to be used for a target nucleic acid where a single nucleotide polymorphism is present, the oligonucleotide probe comprising a reporter region, an anchor region, and a linker region. The reporter region comprises: an oligonucleotide consisting of a sequence perfectly matching when a nucleotide of the single nucleotide polymorphism is a first nucleotide, and mismatching when the nucleotide of the single nucleotide polymorphism is a nucleotide other than the first nucleotide; and a fluorescent dye quenching when the reporter region hybridize to the target nucleic acid.

The present invention provides an oligonucleotide probe for single nucleotide polymorphism detection to be used for a target nucleic acid where a single nucleotide polymorphism is present, the oligonucleotide probe comprising a reporter region, an anchor region, and a linker region. The reporter region comprises: an oligonucleotide consisting of a sequence perfectly matching when a nucleotide of the single nucleotide polymorphism is a first nucleotide, and mismatching when the nucleotide of the single nucleotide polymorphism is a nucleotide other than the first nucleotide; and a fluorescent dye quenching when the reporter region hybridize to the target nucleic acid.