Modified nucleotides
Modified nucleotides, and methods to modify nucleotides with a moiety or label, such as biotin, that permits their detection and results in a modified nucleotide, and methods of use of the modified nucleotide in quantitative and qualitative assays.
1. A compound having the structure (I):
or a salt, conjugate base, tautomer, or ionized form thereof, wherein
P1 is a phosphate group;
P2 is a phosphate group;
Nus is a nucleoside moiety comprising a sugar bound to a purine or pyrimidine base;
Alk is a connecting group having the structure —//—(CH 2 ) m —Y—//— where 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
where
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, and
the leftmost bond is to Alk and the rightmost bond is to Obs; and Obs is an observable label.
2. The compound of claim 1 wherein
the sugar is ribose having a 5′ site, a 3′ site, and a 1′ site,
P1 is attached to ribose at the 5′ site, P2 is attached to ribose at the 3′ site,
and the purine or pyrimidine base is selected from cytosine (C), uracil (U), adenine (A), guanine (G), or inosine (I) and is attached to ribose at the 1′ site.
3. The compound of claim 1 wherein the purine or pyridine base is selected from 1-methyladenine, N6-methyladenine, N6-isopentyladenine, N,N-dimethyladenine, 7-deazaadenine, 2-thiocytosine, 3-methylcytosine, N4-acetylcytosine, 2-thiocytosine, 1-methylguanine, 2-methylguanine, 7-methylguanine, N2,N2-dimethylguanine, 7-deazaguanine, 2-thiouracil, 6-thiopurine, or 2,6-diaminopurine.
4. The compound of claim 1 wherein the observable label is a chromogen, a fluorophore, a mass label, a spin label, a streptavidin-binding label, or a secondary detection label.
5. The compound of claim 1 wherein n is an integer ranging from 2 to 24 inclusive.
6. The compound of claim 1 wherein the sugar is ribose, the purine or pyrimidine base is selected from adenine (A), cytosine (C), guanine (G), uracil (U), or inosine (I), m is 3, n is 4, and the observable label is a streptavidin-binding compound selected from biotin, desthiobiotin, or iminobiotin.
7. The compound of claim 1 wherein the sugar is ribose, the purine or pyrimidine base is cytosine (C),
m is 3, Lnk is
wherein n is 4,
A 2 is
A 2 is
and when present, A 3 is
and Obs is selected from the group consisting of biotin, a fluorophore, and an azide.
8. A method of labeling a ribonucleic acid (RNA), the method comprising
heating RNA in a solution, the solution optionally containing dimethylsulfoxide at a concentration up to 25%, to at least 75° C. up to 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 compound of claim 1 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 claim 1 to the RNA to result in a modified RNA.
9. The method of claim 8 wherein the concentration of PEG is about 15%.
10. The method of claim 8 wherein the molecular weight of PEG is 20,000.
11. The method of claim 8 using the compound of claim 1 .
12. A method of synthesizing the compound of claim 1 , wherein the compound is biotin-polyethylene glycol (PEG)-alkane-3′,5′-cytidine-bisphosphate, the method comprising
reacting propargyltrifluoroacetamide with 5-iodocytidine to result in 5-[3-(trifluoroacetamido)propynyl]cytidine,
converting 5-[3-(trifluoroacetamido)propynyl]cytidine to 5-[3-(trifluoroacetamido)propyl]cytidine, converting 5-[3-(trifluoroacetamido)propyl]cytidine to 5-(3-aminopropyl)cytidine,
reacting 5-(3-aminopropyl)cytidine with NHS-PEG-biotin to result in biotin-PEG-alkane-cytidine,
and
reacting biotin-PEG-alkane-cytidine with diphosphoryl chloride to result in biotin-polyethylene glycol (PEG)-alkane-3′,5′-cytidine-bisphosphate.
13. A kit comprising the compound of claim 1 and instructions for labeling a ribonucleic acid (RNA) with the compound.
14. A kit comprising the compound of claim 1 , wherein Obs is biotin, and instructions for capturing and/or using a ribonucleic acid (RNA) labeled with the compound on an array or chip.
15. A method for assaying a ribonucleic acid (RNA) analyte, the method comprising
labeling an RNA with the compound of claim 1 to result in a modified RNA probe, and
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
detecting the RNA analyte hybridized with the modified RNA probe, wherein hybridization and detection of the modified RNA probe assays the RNA analyte.
16. The method of claim 15 where the assay is at least one of mobility shift, Northern blot, pull-down assay, or in situ hybridization.
17. The method of claim 15 where the detection uses a streptavidin-conjugated reporter molecule.
18. The method of claim 15 where the reporter molecule is selected from the group consisting of enzymes, fluorescent compounds, isotopes, gold particles, and combinations thereof.
19. The method of claim 15 using the compound of claim 1 .
20. A compound having the structure