NUCLEOTIDE ANALOGUES
Disclosed herein, inter alia, are compounds and methods of using the same for the modifying a nucleic acid molecule.
1 . A modified nucleotide comprising a moiety attached to a 3′ oxygen of the nucleotide or nucleoside, wherein the moiety is
2 . The modified nucleotide of claim 1 , comprising a 2′ hydroxyl moiety.
3 . The modified nucleotide of claim 1 , comprising a 2′ hydrogen moiety.
4 . The modified nucleotide of claim 1 , comprising a nucleobase, wherein the nucleobase is a monovalent cytosine, monovalent guanine, monovalent adenine, monovalent thymine, monovalent uracil, monovalent hypoxanthine, monovalent xanthine, monovalent 7-methylguanine, monovalent 5,6-dihydrouracil, monovalent 5-methylcytosine, or monovalent 5-hydroxymethylcytosine.
5 . The modified nucleotide of claim 1 , comprising a nucleobase having the formula:
6 . The modified nucleotide of claim 1 , comprising a nucleobase having the formula:
7 . The modified nucleotide of claim 1 , comprising a nucleobase having the formula:
8 . The modified nucleotide of claim 1 , covalently attached to a fluorophore via a cleavable linker.
9 . The modified nucleotide of claim 8 , wherein said cleavable linker comprises an azido moiety, an allyl moiety, or a disulfide moiety.
10 . The modified nucleotide of claim 1 , wherein the moiety is
11 . The modified nucleotide of claim 1 , wherein the moiety is
12 . The modified nucleotide of claim 1 , wherein the moiety is
13 . The modified nucleotide of claim 1 , wherein the moiety is
14 . The modified nucleotide of claim 1 , wherein the moiety is
15 . The modified nucleotide of claim 1 , wherein the moiety is
16 . A method for removing a moiety attached to a 3′ oxygen of a modified nucleotide, comprising:
contacting a primer oligonucleotide hybridized to a template polynucleotide with the modified nucleotide of claim 1 and a polymerase and binding the modified nucleotide to a complementary nucleotide of said template polynucleotide; and
contacting the modified nucleotide with a cleaving agent comprising palladium, tris-(2-carboxyethyl)phosphine, nitrous acid, tris(3-hydroxypropyl)phosphine), sodium dithionite (Na 2 S 2 O 4 ), or hydrazine (N 2 H 4 ), thereby removing the moiety.
17 . A method of incorporating a compound into a primer, the method comprising combining a polymerase, a primer hybridized to nucleic acid template and the compound within a reaction vessel and allowing said polymerase to incorporate said compound into said primer thereby forming an extended primer, wherein said compound is the modified nucleotide of claim 3 .
18 . A nucleic acid polymerase complex comprising a nucleic acid polymerase, wherein said nucleic acid polymerase is bound to the modified nucleotide of claim 3 .