Silicon containing modified nucleotide analogs
Disclosed herein, inter alia, are silicon containing cleavable linkers and compounds for use in nucleic acid sequencing.
1 . A compound having the formula:
wherein
B is a divalent nucleobase;
R 1 is a 5′-nucleoside protecting group, monophosphate moiety, polyphosphate moiety, or nucleic acid moiety;
R 2 and R 3 are independently 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, polymerase-compatible cleavable moiety, or an —O-polymerase-compatible cleavable moiety;
R 4 is a fluorescent dye moiety; and
L 100 is a divalent linker comprising
wherein
R 5 and R 6 are independently hydrogen, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , 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 7 , R 8 , and R 9 are independently hydrogen, 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.
2 . The compound of claim 1 , wherein R 2 is hydrogen.
3 . The compound of claim 1 , wherein R 1 is a triphosphate moiety.
4 . The compound of claim 1 , wherein B 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.
5 . The compound of claim 1 , having the formula:
6 . The compound of claim 1 , wherein L 100 is -L 101 -L 102 -L 103 -L 104 -L 105 -;
L 101 , L 102 , 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; and
L 103 is
7 . The compound of claim 1 , wherein R 5 and R 6 are independently hydrogen, or substituted or unsubstituted alkyl.
8 . The compound of claim 1 , wherein R 5 and R 6 are independently hydrogen, or unsubstituted C 1 -C 4 alkyl.
9 . The compound of claim 1 , wherein R 7 , R 8 , and R 9 are independently substituted or unsubstituted C 1 -C 6 alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl, substituted or unsubstituted C 3 -C 6 cycloalkyl, substituted or unsubstituted 2 to 8 membered heterocycloalkyl, substituted or unsubstituted C 6 to C 12 aryl, or substituted or unsubstituted 2 to 8 membered heteroaryl.
10 . The compound of claim 1 , wherein R 7 , R 8 , and R 9 are independently substituted or unsubstituted C 1 -C 6 alkyl.
11 . The compound of claim 1 , wherein R 7 , R 8 , and R 9 are unsubstituted C 1 -C 6 alkyl.
12 . The compound of claim 6 , wherein L 100 has the formula:
13 . The compound of claim 6 , wherein L 100 has the formula:
14 . The compound of claim 1 , wherein R 3 is an —O-polymerase-compatible cleavable moiety having the formula
15 . A compound having the formula:
wherein
B is a divalent nucleobase;
R 1 is a 5′-nucleoside protecting group, monophosphate moiety, polyphosphate moiety, or nucleic acid moiety;
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 3 is
R 4 is a fluorescent dye moiety;
L 100 is a divalent linker;
R 5 and R 6 are independently hydrogen, —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , 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 7 , R 8 , and R 9 are independently hydrogen, 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 10 is substituted or unsubstituted alkyl.
16 . 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 fluorescent dye moiety;
(ii) detecting said unique fluorescent dye moiety 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 .
17 . 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 fluorescent dye moiety;
(ii) detecting said unique fluorescent dye moiety 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 15 .
18 . A method of sequencing a nucleic acid comprising:
(i) providing a nucleic acid template hybridized to a primer;
(ii) extending the primer hybridized to said nucleic acid template with a compound of claim 1 ; and
(iii) identifying the compound, so as to sequence the nucleic acid.
19 . A method of incorporating a compound into a primer, the method comprising combining a polymerase, a primer hybridized to a 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 .
20 . A nucleic acid polymerase complex comprising a nucleic acid polymerase, wherein said nucleic acid polymerase is bound to a compound of claim 1 .