Nucleotide cleavable linkers and uses thereof
Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof for sequencing a nucleic acid.
1. A compound having the formula:
wherein,
B is a divalent nucleobase;
R 1 is independently 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 , —Cl 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 or an —O-polymerase-compatible cleavable moiety;
L 101 , 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;
R 100 is —SR 102 or —CN;
R 102 and R 102a are independently hydrogen, halogen, —CCl 3 , —CBr 3 , —CF 3 , —Cl 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; and
R 4 is a detectable moiety;
wherein said 5′-nucleoside protecting group is
R 9 is substituted or unsubstituted C 1 -C 4 alkyl;
R 10 and R 11 are each independently halogen, —CF 3 , —Cl 3 , —CBr 3 , —CHF 2 , —CHCl 2 , —CHI 2 , —CHBr 2 , —OCH 2 F, —OCH 2 Cl, —OCH 2 I, —OCH 2 Br, —OCHF 2 , —CHCl 2 , —OCHI 2 , —OCHBr 2 , —OCF 3 , —OCI 3 , —OCI 3 , —OCBr 3 , —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, —N 3 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl; and
z10 and z11 are each independently an integer from 0 to 5.
2. The compound of claim 1 , wherein R 3 is an —O-polymerase-compatible cleavable moiety.
3. The compound of claim 1 , wherein the polymerase-compatible cleavable moiety is independently -(substituted or unsubstituted alkylene)-SS-(unsubstituted alkyl).
4. The compound of claim 1 , wherein the polymerase-compatible cleavable moiety is independently -(halo-substituted or unsubstituted C 1 -C 3 alkylene)-SS-(unsubstituted C 1 -C 4 alkyl).
5. The compound of claim 1 , wherein the polymerase-compatible cleavable moiety is independently:
6. The compound of claim 1 , wherein the polymerase-compatible cleavable moiety is independently:
7. The compound of claim 1 , wherein R 2 is hydrogen or —OH.
8. The compound of claim 1 , wherein R 1 is a monophosphate moiety, a polyphosphate moiety, or a nucleic acid moiety.
9. The compound of claim 1 , wherein
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.
10. The compound of claim 1 , wherein;
L 101 , L 103 , L 104 , and L 105 are independently a bond, 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
R 102 and R 102a are independently hydrogen or unsubstituted alkyl.
11. The compound of claim 1 , wherein
L 101 is independently a substituted or unsubstituted C 1 -C 4 alkylene or substituted or unsubstituted 8 to 20 membered heteroalkylene;
L 103 is independently a bond or substituted or unsubstituted 2 to 10 membered heteroalkylene;
L 104 is independently a bond, substituted or unsubstituted 4 to 18 membered heteroalkylene, or substituted or unsubstituted phenylene;
L 105 is independently bond or substituted or unsubstituted 4 to 18 membered heteroalkylene; and
R 102 is unsubstituted C 1 -C 4 alkyl; and
R 102a is hydrogen or unsubstituted methyl.
12. The compound of claim 1 , wherein
L 101 , L 103 , 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;
L 104 is unsubstituted phenylene; and
R 102 and R 102a are independently hydrogen or unsubstituted alkyl.
13. The compound of claim 1 , wherein
L 101 is independently a substituted or unsubstituted C1-C 4 alkylene or substituted or unsubstituted 8 to 20 membered heteroalkylene;
L 103 is independently a bond or substituted or unsubstituted 2 to 10 membered heteroalkylene;
L 104 is independently an unsubstituted phenylene;
L 105 is independently bond or substituted or unsubstituted 4 to 18 membered heteroalkylene; and
R 102 is unsubstituted C 1 -C 4 alkyl; and
R 102a is hydrogen or unsubstituted methyl.
14. The compound of claim 1 , wherein -(L 101 )-OC(SSR 102 )(R 102a )-(L 103 )-(L 104 )-(L 105 )- is
15. The compound of claim 1 , wherein R 4 is a fluorescent dye moiety.
16. The compound of claim 1 , having the formula:
wherein
R 3 is an —O-polymerase-compatible cleavable moiety.
17. The compound of claim 1 , having the formula:
wherein R 3A is a polymerase-compatible cleavable moiety.
18. The compound of claim 17 , wherein
19. The compound of claim 17 , wherein R 3A is independently:
20. The compound of claim 1 , having the formula: