Detectable labeled nucleoside analogs and methods of use thereof

A compound of formula II:

• 104
• alone or in combination with a counterion thereof or a stable salt, solvate, clathrate or mixture thereof, wherein:
• base is
• 105
• wherein sugar is covalently bonded to N1 of the base;
• wherein R1 is —NHC(O)NH2, —H, —NH2, —OH, —O(alkyl), alkyl, or CO2H;
• wherein R2 is —H or alkyl;
• each of X, Y, and Z is independently H, —OH, —O-alkyl, —SH, —SR4, —NHR4, —NR4R5,
• 106
• wherein R3 is —H or metal;
• R4 is —H or alkyl;
• R5 is —H or alkyl;
• linker is (CH2CH2O)n, (CH2O)n or (CH2)n;
• wherein n is an integer from 1 to 30;
• Q is O, S, or NH;
• and
• label is a colorimetric compound, a chemiluminescent compound, a bioluminescent compound, a fluorescent compound, a non- or weakly fluorescent compound, or a quencher.

A compound of formula III:

• 112
• alone or in combination with a counterion thereof or a stable salt, solvate, clathrate or mixture thereof, wherein each of X, Y, and Z is independently —H, —OH, —O(alkyl), —SH, —SR4, —NHR4, —NRR5,
• 113
• wherein R3 is —H or metal;
• R4 is —H or alkyl;
• and R5 is —H or alkyl.

A compound of formula IV:

• 115
• wherein X, Y, and Z are independently H, OH,
• 116
• wherein R3 is H or metal.

A compound of formula V:

• 117
• wherein X, Y, and Z are independently H, OH,
• 118
• wherein R3 is H or metal.

A compound of formula VI:

• 119
• wherein X, Y, and Z are independently H, OH,
• 120
• wherein R3 is H or metal.

A compound of formula VII:

• 121
• wherein X, Y, and Z are independently H, OH,
• 122
• wherein R3 is H or metal.

A compound of formula VIII:

• 123
• wherein X, Y, and Z are independently H, OH,
• 124
• wherein R3 is H or metal.

A compound of formula IX:

• 125
• wherein X, Y, and Z are independently H, OH,
• 126
• wherein R3 is H or metal.

A compound of formula X:

• 127
• wherein X, Y, and Z are independently H, OH,
• 128
• wherein R3 is H or metal.

A compound of formula XI:

• 129
• wherein X, Y, and Z are independently H, OH,
• 130
• wherein R3 is H or metal.

An oligonucleotide comprising a detectable label of formula (XXI):

• 140
• alone or in combination with a counterion thereof or a stable salt, solvate, clathrate or mixture thereof, wherein:
• sugar is a ribose, deoxyribose or a ribose sugar analog;
• base is
• 141
• wherein sugar is covalently bonded to N1 of the base;
• wherein R1 is —NHC(O)NH2, —H, —NH2, —OH, —O(alkyl), alkyl, or CO2H;
• wherein R2 is —H or alkyl;
• linker is (CH2CH2O)n, (CH2O)n or (CH2)n;
• wherein n is an integer from 1 to 30;
• and
• label is a colorimetric, chemiluminescent, bioluminescent, a fluorescent compound, a non- or weakly fluorescent compound, or a quencher.

An oligonucleotide comprising a detectable label of formula XXII:

• 142
• alone or in combination with a counterion thereof or a stable salt, solvate, clathrate or mixture thereof, wherein:
• base is
• 143
• wherein sugar is covalently bonded to N1 of the base;
• wherein R1 is —NHC(O)NH2, —H, —NH2, —OH, —O(alkyl), alkyl, or CO2H;
• wherein R2 is —H or alkyl;
• each of X, Y, and Z is independently —H, —OH, —O(alkyl), —SH, —SR4, —NHR4, —NR4R5,
• 144
• wherein R3 is —H or metal;
• R4 is —H or alkyl;
• R5 is —H or alkyl;
• linker is (CH2CH2O)n, (CH2O)n or (CH2)n;
• wherein n is an integer from 1 to 30;
• Q is O, S, or NH;
• and
• label is a colorimetric, chemiluminescent, bioluminescent, a fluorescent compound, a non- or weakly fluorescent compound, or a quencher.

A detectable label of formula XXIII:

• 150
• wherein X, Y, and Z are independently H, OH,
• 151
• wherein R3 is H or metal.

A detectable label of formula XXIV:

• 152
• wherein X, Y, and Z are independently H, OH,
• 153
• wherein R3 is H or metal.

A detectable label of formula XXV:

• 154
• wherein X, Y, and Z are independently H, OH,
• 155
• wherein R3 is H or metal.

A detectable label of formula XXVI:

• 156
• wherein X, Y, and Z are independently H, OH,
• 157
• wherein R3 is H or metal.

A detectable label of formula:

• 158
• wherein X, Y, and Z are independently H, OH,
• 159
• wherein R3 is H or metal.

A detectable label of formula XXVIII:

• 160
• wherein X, Y, and Z are independently H, OH,
• 161
• wherein R3 is H or metal.

A detectable label of formula XXIX:

• 162
• wherein X, Y, and Z are independently H, OH,
• 163
• wherein R3 is H or metal.

A detectable label of formula XXX:

• 164
• wherein X, Y, and Z are independently H, OH,
• 165
• wherein R3 is H or metal.

A detectable label of formula XXXI:

• 166
• wherein X, Y, and Z are independently H, OH,
• 167
• wherein R3 is H or metal.

A method for detecting the presence or absence of a target nucleic acid in a test sample, comprising:

• a) contacting the test sample with a composition comprising an oligo- or poly nucleotide probe wherein the oligo- or polynucleotide probe comprises a detectable label of formula:
• 177
• base is
• 178
• wherein sugar is covalently bonded to N1 of the base;
• wherein R1 is —NHC(O)NH2, —H, —NH2, —OH, —O(alkyl), alkyl, or CO2H;
• wherein R2 is —H or alkyl;
• each of X, Y, and Z is independently —H, —OH, —O-alkyl, —SH, —SR4, —NHR4, —NR4R5,
• 179
• wherein R3 is H or metal;
• R4 is —H or alkyl;
• R5 is —H or alkyl;
• linker is (CH2CH2O)n, (CH2O)n or (CH2)n;
• wherein n is an integer from 1 to 30;
• Q is O, S, or NH;
• label is a colorimetric, chemiluminescent, bioluminescent, a fluorescent compound, or a non- or weakly fluorescent compound;
• wherein the oligonucleotide probe is capable of selectively or specifically hybridizing with the target nucleic acid under conditions of moderate stringency;
• optionally exposing the sample to light of said excitable wavelength;
• and
• b) detecting whether said contacting produces a change in color or fluorescence emission of the composition;
• such that a change in color or fluorescence emission of the composition indicates that the target nucleic acid is present in the test sample.