Abstract: This disclosure relates to methods, compositions, and related apparatuses for detection and quantification of nucleic acid molecules associated with a solid surface. Methods can include detecting or quantifying at least one nucleic acid molecule associated with a surface by contacting the at least one nucleic acid molecule with a fluorophore, wherein the fluorophore emits increased fluorescence at a wavelength when in contact with nucleic acid molecule, and detecting or measuring fluorescence from the fluorophore at the wavelength. Compositions can comprise a fluorophore and a nucleic acid molecule, wherein the nucleic acid molecule is associated with a surface, and the fluorophore has the property of emitting increased fluorescence at a wavelength when in contact with a nucleic acid molecule.

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.

Abstract: Substituted unsymmetrical cyanine dyes are provided herein, including kits, assays systems and methods for their use in the detection of RNA compounds (e.g., miRNA).

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.

Abstract: Cyanine dye compounds having a negatively charged substituent that are nucleic acid stains, particularly for fluorescent staining of DNA, including compounds having the formula wherein W forms one or two fused 5- or 6-membered aromatic rings, ? has a value of 0 or 1, n has a value of 0, or 1, X is O, S, or Se, and D is a pyridinium, or quinolinium moiety, provided that the compound has at least one negatively charged substituent.

Abstract: Cyanine dye compounds having a negatively charged substituent that are nucleic acid stains, particularly for fluorescent staining of DNA, including compounds having the formula wherein W forms one or two fused 5- or 6-membered aromatic rings, ? has a value of 0 or 1, n has a value of 0, or 1, X is O, S, or Se, and D is a pyridinium, or quinolinium moiety, provided that the compound has at least one negatively charged substituent.

Abstract: Cyanine dye compounds having a negatively charged substituent that are nucleic acid stains, particularly for fluorescent staining of DNA, including compounds having the formula wherein W forms one or two fused 5- or 6-membered aromatic rings, a has a value of 0 or 1, n has a value of 0, or 1, X is O, S, or Se, and D is a pyridinium, or quinolinium moiety, provided that the compound has at least one negatively charged substituent.

Abstract: Cyanine dye compounds having a substituted methine moiety that are nucleic acid stains, particularly for fluorescent staining of RNA, including compounds having the formula where R1 is a C1-C6 alkyl, sulfoalkyl, carboxyalkyl or C1-C6 alkoxy; each R2 is independently selected from the group consisting of H, C1-C6 alkyl, C1-C6 alkoxy, fused benzo, trifluoromethyl, amino, sulfo, carboxy and halogen, that is optionally further substituted; at least one of R3, R4, and R5 is an alkyl, aryl, heteroaryl, cyclic, or heterocyclic moiety that is optionally substituted by alkyl, amino, aminoalkyl, carboxy, nitro, or halogen; and the remaining R3, R4 or R5 are hydrogen; X is S, O, or Se; and D is a substituted or unsubstituted pyridinium, quinolinium or benzazolium moiety.