Modified nucleotides and uses thereof
Disclosed herein, inter alia, are compounds, modified nucleotides, compositions, and methods of using the same.
1 . A compound having the formula:
wherein
B 1 is a nucleobase;
R 1 is a polyphosphate moiety, 5′-O-nucleoside protecting group, monophosphate moiety, nucleic acid moiety, hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 , —CHI 2 , —CH 2 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC(O)NHNH 2 , —NHC(O)NH 2 , —NHSO 2 H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 , —OCHI 2 , —OCHF 2 , —OCH 2 Cl, —OCH 2 Br, —OCH 2 I, —OCH 2 F, —N 3 , —SF 5 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R 2 is hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —CI 3 , —CHCl 2 , —CHBr 2 , —CHF 2 , —CHI 2 , —CH 2 Cl, —CH 2 Br, —CH 2 F, —CH 2 I, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —NHC(O)NHNH 2 , —NHC(O)NH 2 , —NHSO 2 H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCCl 3 , —OCF 3 , —OCBr 3 , —OCI 3 , —OCHCl 2 , —OCHBr 2 , —OCHI 2 , —OCHF 2 , —OCH 2 Cl, —OCH 2 Br, —OCH 2 I, —OCH 2 F, —N 3 , —SF 5 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, or a polymerase-compatible cleavable moiety;
R 7 is unsubstituted or substituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl; and
R 8 is unsubstituted C 1 -C 6 alkyl.
2 . The compound of claim 1 , wherein R 2 is hydrogen.
3 . The compound of claim 1 , wherein R 1 is —OH, a 5′-O-nucleoside protecting group, monophosphate moiety, polyphosphate moiety, or nucleic acid moiety.
4 . The compound of claim 1 , wherein R 1 is a triphosphate moiety.
5 . The compound of claim 1 , wherein R 8 is unsubstituted C 1 -C 4 alkyl.
6 . The compound of claim 1 , wherein R 8 is unsubstituted methyl or unsubstituted ethyl.
7 . The compound of claim 1 , wherein B 1 is a cytosine or a derivative thereof, guanine or a derivative thereof, adenine or a derivative thereof, thymine or a derivative thereof, uracil or a derivative thereof, hypoxanthine or a derivative thereof, xanthine or a derivative thereof, 7-methylguanine or a derivative thereof, 5,6-dihydrouracil or a derivative thereof, 5-methylcytosine or a derivative thereof, or 5-hydroxymethylcytosine or a derivative thereof.
8 . The compound of claim 1 , wherein B 1 is
9 . The compound of claim 1 , wherein
B 1 is —B-L 100 -R 4 ;
B is a divalent cytosine or a derivative thereof, divalent guanine or a derivative thereof, divalent adenine or a derivative thereof, divalent thymine or a derivative thereof, divalent uracil or a derivative thereof, divalent hypoxanthine or a derivative thereof, divalent xanthine or a derivative thereof, divalent 7-methylguanine or a derivative thereof, divalent 5,6-dihydrouracil or a derivative thereof, divalent 5-methylcytosine or a derivative thereof, or divalent 5-hydroxymethylcytosine or a derivative thereof;
L 100 is a divalent linker; and
R 4 is a detectable moiety.
10 . The compound of claim 9 , wherein L 100 is a divalent linker comprising
wherein R 9 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
11 . The compound of claim 9 , wherein L 100 is a divalent linker comprising
wherein R 102 is unsubstituted C 1 -C 4 alkyl.
12 . The compound of claim 9 , wherein L 100 is -L 101 -L 102 -L 103 -L 104 -L 105 -;
L 101 , L 102 , L 103 , L 104 , and L 105 are independently a bond, —NH—, —O—, —C(O)—, —C(O)NH—, —NHC(O)—, —NHC(O)NH—, —C(O)O—, —OC(O)—, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
13 . The compound of claim 12 , wherein L 100 is
wherein
R 9 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and
R 102 is unsubstituted C 1 -C 4 alkyl.
14 . The compound of claim 12 , wherein L 100 is
wherein
R 9 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and
R 102 is unsubstituted C 1 -C 4 alkyl.
15 . The compound of claim 9 , wherein L 100 is
16 . The compound of claim 9 , wherein L 100 is
17 . The compound of claim 9 , having the formula:
wherein L 100 is a cleavable linker.
18 . The compound of claim 17 , wherein R 7 is substituted or unsubstituted cycloalkyl.
19 . The compound of claim 17 , wherein R 7 is substituted or unsubstituted heterocycloalkyl.
20 . The compound of claim 17 , wherein L 100 is
wherein
R 9 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R 102 is unsubstituted C 1 -C 4 alkyl; and
L 103 , L 104 , and L 105 are independently a bond, —NH—, —O—, —C(O)—, —C(O)NH—, —NHC(O)—, —NHC(O)NH—, —C(O)O—, —OC(O)—, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
21 . The compound of claim 1 , wherein R 7 is substituted or unsubstituted cycloalkyl.
22 . The compound of claim 1 , wherein R 7 is unsubstituted cycloalkyl.
23 . The compound of claim 1 , wherein R 7 is substituted or unsubstituted heterocycloalkyl.
24 . The compound of claim 1 , wherein R 7 is unsubstituted cycloalkyl or unsubstituted heterocycloalkyl.
25 . The compound of claim 1 , wherein R 7 is
26 . A nucleic acid polymerase complex comprising a nucleic acid polymerase, wherein said nucleic acid polymerase is bound to a compound of claim 1 .
27 . A method for sequencing a nucleic acid, comprising:
(i) incorporating in series with a nucleic acid polymerase, within a reaction vessel, one of four different compounds into a primer to create an extension strand, wherein said primer is hybridized to said nucleic acid and wherein each of the four different compounds comprises a unique detectable label;
(ii) detecting said unique detectable label of each incorporated compound, so as to thereby identify each incorporated compound in said extension strand, thereby sequencing the nucleic acid;
wherein each of said four different compounds is independently a compound of claim 1 .
28 . 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 a compound of claim 1 .