The present invention relates to a new class of substituted aza-triangulenium fluorescent dyes having a hydroxy group attached to an aryl as quenching group. The new substituted aza-triangulenium fluorescent dyes may be attached to a linker, conjugated to carrier molecule such as e.g. a protein, a nucleic acid, a lipid, or a saccharide, or deposited or immobilized on solid support materials. The substituted aza-triangulenium fluorescent dyes are useful for various purposes, including use in sensors for monitoring or determining the concentration of analytes, such as H.sup.+(pH), Na.sup.+, K.sup.+, Ca.sup.2+, O.sub.2, CO.sub.2, H.sub.2O.sub.2, ionic strength, redox potentials, metal ions, and metabolites.

According to the present teachings, methods and compositions are provided that utilize at least one reference dye of formula (I):

##STR00001##

In some embodiments, a method comprises measuring a detection signal of a reporter dye and at least one reference dye of formula (I). In some embodiments, a composition comprises a reference dye of formula (1), a buffer, a selection of nucleotides and a protein.

According to the present teachings, methods and compositions are provided that utilize at least one reference dye of formula (I):

##STR00001##

In some embodiments, a method comprises measuring a detection signal of a reporter dye and at least one reference dye of formula (I). In some embodiments, a composition comprises a reference dye of formula (1), a buffer, a selection of nucleotides and a protein.

A fluorescent dye and quencher mixture for reporting on nucleic acid amplification from a sample includes a fluorescent intercalating dye, a dye sequestering or quenching agent such as hydroxynapthol blue (HNB) or caffeine, and primers, dNTPs, and a nucleic acid polymerizing enzyme or fragment thereof. The presence of the dye in combination with the dye sequestering or quenching agent improves the overall dynamic range of the fluorescent signal as well as shortens the time needed for visualization or image capture of amplified nucleic acid. The fluorescent dye and quencher mixture also enables the detection of nucleic acids in samples having low copy numbers.

A fluorescent dye and quencher mixture for reporting on nucleic acid amplification from a sample includes a fluorescent intercalating dye, a dye sequestering or quenching agent such as hydroxynapthol blue (HNB) or caffeine, and primers, dNTPs, and a nucleic acid polymerizing enzyme or fragment thereof. The presence of the dye in combination with the dye sequestering or quenching agent improves the overall dynamic range of the fluorescent signal as well as shortens the time needed for visualization or image capture of amplified nucleic acid. The fluorescent dye and quencher mixture also enables the detection of nucleic acids in samples having low copy numbers.

The presently-disclosed subject matter includes azetidine-substituted fluorescent compounds, where the compounds may be used as probes, dyes, tags, and the like. The presently-disclosed subject matter also includes kits comprising the same as well as methods for using the same to detect a target substance.

The presently-disclosed subject matter includes azetidine-substituted fluorescent compounds, where the compounds may be used as probes, dyes, tags, and the like. The presently-disclosed subject matter also includes kits comprising the same as well as methods for using the same to detect a target substance.

In one aspect, the disclosure relates to xanthene-, thiazine-, and oxazine-based dyes containing a phosphinate ester group and having near-infrared (NIR) absorption and methods of making the same. The fluorescence lifetimes and stabilities of the dyes can be tuned by modifying the molecule cores, making them suitable for a variety of chemical labeling, imaging, and other theranostic applications. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present disclosure.

Compounds of formula I are disclosed: ##STR00001##
wherein X.sup.1, X.sup.2, X.sup.3, X.sup.4 are independently H, F, Cl, Br, I, CN, NO.sub.2, OR.sup.1, SR.sup.1, NR.sup.1R.sup.2, COR.sup.1, COOR.sup.1, CONR.sup.1R.sup.2, PO.sub.3R.sup.1R.sup.2, SO.sub.2R.sup.1, SO.sub.3R.sup.1 or R.sup.3; R.sup.1 and R.sup.2 are, e.g., H, alkyl or aryl or optionally a ring; R.sup.3 is, e.g., alkyl, alkenyl, alkynyl, aryl or cycloalkyl; Y is OR.sup.1, NR.sup.1R.sup.2, or NR.sup.1R.sup.3; Q is O, S, SO.sub.2, NR, C(R.sup.3).sub.2, Si(R.sup.3).sub.2, Ge(R.sup.3).sub.2, P(O)R.sup.3 or P(O)OR.sup.3; Q and X.sup.1 can optionally form part of a ring; L and M are independently OR.sup.1, SR.sup.1, NR.sup.1R.sup.2 and R.sup.3; L and M can optionally form part of a ring; Z is O, S, NR.sup.1, CR.sup.1R.sup.3 or aryl; and Z and X.sup.4 can optionally form part of a ring.

Compounds of formula I are disclosed: ##STR00001##
wherein X.sup.1, X.sup.2, X.sup.3, X.sup.4 are independently H, F, Cl, Br, I, CN, NO.sub.2, OR.sup.1, SR.sup.1, NR.sup.1R.sup.2, COR.sup.1, COOR.sup.1, CONR.sup.1R.sup.2, PO.sub.3R.sup.1R.sup.2, SO.sub.2R.sup.1, SO.sub.3R.sup.1 or R.sup.3; R.sup.1 and R.sup.2 are, e.g., H, alkyl or aryl or optionally a ring; R.sup.3 is, e.g., alkyl, alkenyl, alkynyl, aryl or cycloalkyl; Y is OR.sup.1, NR.sup.1R.sup.2, or NR.sup.1R.sup.3; Q is O, S, SO.sub.2, NR, C(R.sup.3).sub.2, Si(R.sup.3).sub.2, Ge(R.sup.3).sub.2, P(O)R.sup.3 or P(O)OR.sup.3; Q and X.sup.1 can optionally form part of a ring; L and M are independently OR.sup.1, SR.sup.1, NR.sup.1R.sup.2 and R.sup.3; L and M can optionally form part of a ring; Z is O, S, NR.sup.1, CR.sup.1R.sup.3 or aryl; and Z and X.sup.4 can optionally form part of a ring.