Modified nucleotides methods and kits

1. A method of quantitating a nucleic acid or an oligonucleotide comprising:

a) adding to a nucleic acid or an oligonucleotide, a detectable modified nucleotide of structure II:

a salt, a conjugate base, a tautomer, or an ionized form thereof, wherein

Base* is a purine or pyrimidine base;

R is H, OH, CH 3 or a hydroxyl protecting group;

Alk is a connecting group having the structure -//—(CH 2 ) m —Y—//- wherein Y is a bond or bond forming group selected from

and

m is an integer ranging from 3 to 6 inclusive, and wherein the leftmost bond is to Nus and the rightmost bond is to Lnk;

Lnk is a linking group having the structure

wherein

n is an integer ranging from 2 to 48 inclusive;

A 1 is a bond forming group selected from

A 2 is a bond forming group selected from

A 3 , when present, is a bond forming group selected from

and X is a cleavable group that can undergo silicon-carbon cleavage, nucleophilic cleavage, redox cleavage, photochemical cleavage, enzymatic cleavage, or exchange-based cleavage; Z is a branching group that contains a crosslinking agent; and the leftmost bond is to Alk and the rightmost bond is to Obs; and Obs is an observable label; and

b) quantitating the nucleic add based on quantifying the detectable modified nucleotide.

2. The method of claim 1 , wherein one molecule of the observable detectable label is added per oligonucleotide or nucleic acid.

3. The method of claim 1 , wherein the observable label is a chromogen, a fluorophore, a mass label, a spin label, a mass tag, a streptavidin-binding label, biotin, a derivative of biotin, desthiobiotin, an azide, an alkyne, an aldehyde, a diene, an amine, a hydrazide, a disulfide, a polyethyleneglycol (PEG), or a secondary detection label.

4. The method of claim 1 , wherein the nucleic acid is a RNA or the oligonucleotide is a ribonucleotide.

5. The method of claim 1 , wherein the oligonucleotide or the nucleic acid is added to the detectable modified nucleotide by ligation, nick translation, random priming, polymerase chain reaction (PCR), 3′-end labeling, or by transcribing RNA using SP6, T3, or T7 RNA polymerases.

6. The method of claim 1 , wherein the nucleic acid is a RNA and the detectable modified nucleotide is added by:

heating RNA in a solution, the solution optionally containing dimethylsulfoxide at a concentration up to 25%, to a temperature of about 75° C. to about 95° C. then cooling the heated RNA for at least one minute to less than 10° C., and,

contacting the heated and cooled RNA with the detectable modified nucleotide of structure (II) under reaction conditions using T4 RNA ligase and including PEG having molecular weight between about 1500 and 24,000 inclusive and at a concentration ranging from 5% PEG to 20% PEG inclusive to ligate the compound of structure (II) to the RNA to result in a detectable modified RNA.

7. The method of claim 6 , wherein the concentration of PEG is about 15%.

8. The method of claim 6 , wherein the molecular weight of PEG is 20,000.

9. A method for assaying a ribonucleic acid (RNA) analyte, the method comprising:

a) labeling an RNA with the detectable modified nucleotide of structure (II)

a salt, a conjugate base, a tautomer, or an ionized form thereof, wherein

Base* is a purine or pyrimidine base;

R is H, OH, CH 3 , or a hydroxyl protecting group;

Alk is a connecting group having the structure -//—(CH 2 ) m —Y—//- wherein Y is a bond or bond forming group selected from

and

m is an integer ranging from 3 to 6 inclusive, and wherein the leftmost bond is to Nus and the rightmost bond is to Lnk;

Lnk is a linking group having the structure

wherein

n is an integer ranging from 2 to 48 inclusive;

A 1 is a bond forming group selected from

A 2 is a bond forming group selected from

A 3 , when present, is a bond forming group selected from

and X is a cleavable group that can undergo silicon-carbon cleavage, nucleophilic cleavage, redox cleavage, photochemical cleavage, enzymatic cleavage, or exchange-based cleavage; Z is a branching group that contains a crosslinking agent; and the leftmost bond is to Alk and the rightmost bond is to Obs; and Obs is an observable label;

to form a modified RNA probe,

b) contacting the modified RNA probe with a sample containing the RNA analyte under conditions to hybridize the modified RNA probe with the RNA analyte, and

c) detecting the RNA analyte hybridized with the modified RNA probe, wherein hybridization and detection of the modified RNA probe assays the RNA analyte.

10. The method of claim 9 wherein the assay is chosen from at least one of mobility shift, Northern blot, pull-down assay, protein-RNA interaction, and in situ hybridization.

11. The method of claim 9 wherein the detection uses a streptavidin-conjugated reporter molecule.

12. The method of claim 11 wherein the reporter molecule is an enzyme, a fluorescent compound, an isotope, a gold particle, or combinations thereof.

13. The method of claim 1 , wherein the nucleic acid or oligonucleotide is bound to or interacts with a protein.

14. The method of claim 13 , wherein the protein is an RNA binding protein or a protein that can interact with a RNA.

15. The method of claim 1 wherein the detectable modified nucleotide is chosen from

16. The method of claim 9 wherein the detectable modified nucleotide is chosen from