Modified

1. A method of extending a primer, said method comprising contacting a primer hybridized to a template polynucleotide with a nucleotide and extending said primer with a polymerase by incorporating the modified nucleotide to form an extended primer, wherein the polymerase comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 1; and further comprises:

an alanine at amino acid position 411 or an amino acid functionally equivalent to amino acid position 411;

a glycine at amino acid position 412 or an amino acid functionally equivalent to amino acid position 412; and

a proline at amino acid position 413 or an amino acid functionally equivalent to amino acid position 413; and

an alanine or glycine at amino acid position 93 or an amino acid functionally equivalent to amino acid position 93.

2. The method of claim 1 , wherein the polymerase further comprises an alanine substitution mutation at position 141 and an alanine substitution mutation at position 143.

3. The method of claim 1 , wherein the polymerase further comprises an alanine substitution mutation at position 144.

4. The method of claim 1 , wherein the polymerase further comprises at least one of the following:

an alanine or histidine at amino acid position 36 or an amino acid position functionally equivalent to amino acid position 36;

an alanine at amino acid position 129 or an amino acid position functionally equivalent to amino acid position 129;

an alanine at amino acid position 141 or an amino acid position functionally equivalent to amino acid position 141;

an alanine at amino acid position 143 or an amino acid position functionally equivalent to amino acid position 143;

an alanine at amino acid position 144 or an amino acid position functionally equivalent to amino acid position 144;

a glutamic acid at amino acid position 152 or an amino acid position functionally equivalent to amino acid position 152;

a glutamic acid or threonine at amino acid position 153 or an amino acid position functionally equivalent to amino acid position 153;

a threonine at amino acid position 155 or an amino acid position functionally equivalent to amino acid position 155;

an aspartic acid at amino acid position 157 or an amino acid position functionally equivalent to amino acid position 157;

an alanine at amino acid position 215 or an amino acid position functionally equivalent to amino acid position 215;

an isoleucine at amino acid position 303 or an amino acid position functionally equivalent to amino acid position 303; or

a methionine at amino acid position 307 or an amino acid position functionally equivalent to amino acid position 307.

5. The method of claim 1 , wherein the polymerase further comprises at least one of the following:

an alanine at amino acid position 317 or an amino acid position functionally equivalent to amino acid position 317;

a phenylalanine at amino acid position 381 or an amino acid position functionally equivalent to amino acid position 381;

a tryptophan at amino acid position 479 or an amino acid position functionally equivalent to amino acid position 479;

an alanine at amino acid position 480 or an amino acid position functionally equivalent to amino acid position 480;

an alanine at amino acid position 481 or an amino acid position functionally equivalent to amino acid position 481;

a valine at amino acid position 488 or an amino acid position functionally equivalent to amino acid position 488;

a serine at amino acid position 517 or an amino acid position functionally equivalent to amino acid position 517;

an isoleucine at amino acid position 593 or an amino acid position functionally equivalent to amino acid position 593;

an alanine at amino acid position 605 or an amino acid position functionally equivalent to amino acid position 605;

or a leucine at amino acid position 642 or an amino acid position functionally equivalent to amino acid position 642.

6. The method of claim 1 , wherein template polynucleotide comprises DNA.

7. The method of claim 1 , wherein the nucleotide comprises a detectable label and a reversible terminator moiety.

8. The method of claim 1 , wherein nucleotide does not include a detectable label.

9. The method of claim 7 , wherein the reversible terminator moiety comprises an azido moiety or a disulfide moiety.

10. The method of claim 7 , wherein the nucleotide has the formula

wherein the Base is a nucleobase, R 3 is a polyphosphate, and R′ is a reversible terminator having the formula:

wherein R A and R B are hydrogen or alkyl and R C is the remainder of the reversible terminator.

11. The method of claim 7 , wherein the reversible terminator moiety comprises

12. The method of claim 7 , wherein the reversible terminator moiety comprises

13. The method of claim 1 , wherein the nucleotide has the formula:

wherein

B is a nucleobase;

L 2 and L 3 are independently cleavable linker;

L 4 is 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;

R 2 is hydrogen or —OH;

R 3 is a polyphosphate;

R 4 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 5 is a detectable label, an anchor moiety, or affinity anchor moiety;

R 12 is a complementary affinity anchor moiety binder;

R 13 is a detectable label;

X 1 and X 2 are independently hydrogen, halogen, —N 3 , or —CN, wherein at least wherein at least one of X 1 or X 2 is halogen, —N 3 , or —CN; and

the symbol “----” is a non-covalent bond.

14. The method of claim 1 , wherein contacting the primer occurs at about 40° C. to about 80° C.

15. The method of claim 1 , wherein contacting the primer occurs at about 50° C. to about 70° C.

16. The method of claim 1 , wherein contacting the primer occurs at about 55° C. to about 65° C.

17. The method of claim 1 , wherein the polymerase further comprises an amino acid substitution mutation at position 36, 129, 141, 143, 144, 152, 153, 155, 157, 209, 210, 213, 214, 215, 276, 277, 303, 307, 313, 317, 479, 480, 481, 488, 517, 593, 605, or 642 of SEQ ID NO: 1.

18. The method of claim 1 , wherein the polymerase is capable of incorporating modified nucleotides at an increased rate of 1-fold to 10-fold relative to the rate of incorporation of its wild type polymerase.