Compositions and methods for enhanced synthesis of nucleic acid molecules

• US 6,787,305 B1
• Filed: 03/12/1999
• Issued: 09/07/2004
• Est. Priority Date: 03/13/1998
• Status: Expired due to Term

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Invitrogen Corp. (Thermo Fisher Scientific Incorporated)
• Inventors: Gebeyehu, Gulilat, Jessee, Joel A., Schuster, David, Li, Wu-Bo, Xia, Jiulin
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/266,935
• Time in Patent Office: 2,006 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 536/22.1, 536/23.1, 536/25.3
• US Class Current: 435/6.12
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer

Abstract

The present invention is directed to compositions and methods for enhancing synthesis of nucleic acid molecules, particularly GC-rich nucleic acid molecules. Specifically, the invention provides compositions comprising one or more nitrogen-containing organic compounds having a formula selected from the group consisting of formula I and formula II (or salts or derivatives thereof), preferably 4-methylmorpholine N-oxide or betaine (carboxymethyltrimethylammonium), and further comprising one or more compounds selected from the group consisting of proline and an N-alkylimidazole compound, and more preferably proline, 1-methyliimidazole or 4-methylimidazole. The invention further relates to methods for enhanced, high-fidelity synthesis of nucleic acid molecules, including via amplification (particularly PCR), reverse transcription, and sequencing methods. The invention also relates to nucleic acid molecules synthesized by these methods, to fragments or derivatives thereof, and to vectors and host cells comprising such nucleic acid molecules, fragments, or derivatives. The invention also relates to kits for synthesizing, amplifying, reverse transcribing or sequencing nucleic acid molecules comprising one or more of the compositions of the invention.

Claims

1. A composition for use in synthesizing a nucleic acid molecule, comprising one or more enzymes having nucleic acid polymerase activity and one or more compounds having a chemical formula selected from the group consisting of formula I or formula II, or a salt thereof, wherein said compound is not betaine, an amino acid, or a saccharide:

Formula I;

where A is

where X is

where N is positively charged;

wherein q=1 to 100,000, wherein when q=2 to 100,000 each monomer of formula I may be the same as or different from the other monomers of formula I;

wherein Z may be the same as or different from Y;

wherein each Y and Z are independently selected from the group consisting of —

OH, —

NH₂, —

SH, —

PO₃H, —

CO₂H, —

SO₃H and hydrogen;

wherein f is an integer from 0 to 2, m is an integer from 0 to 20 and e is an integer from 0 to 2;

wherein R₄, R₅, and R₆ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, mercaptan, thiol, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups, and d is an integer from 0 to 2;

wherein a, b, and c are independently an integer from 0 to 1, with the proviso that no more than two of a, b, and c are zero;

wherein R₁, R₂ and R₃ may be the same or different and are independently selected from the group consisting of;

with the proviso that no more than two of A, R₁, R₂ and R₃ are selected from the group consisting of hydrogen, methyl, ethyl and propyl; and

with the proviso that if one, and only one, of R₁, R₂ and R₃ is ═

O, then A is none of hydrogen, methyl, ethyl and propyl;

wherein each R₇ and W may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups;

g is an integer from 0 to 2 and n is an integer from 0 to 20, with the proviso that if two of R₁, R₂, and R₃ are ═

O, then the other is not ═

O;

Formula II;

wherein Formula II is saturated or unsaturated;

wherein q=1 to 100,000, wherein when q=2 to 100,000, each monomer of formula II may be the same as or different from each other monomer of formula II;

wherein X is selected from the group consisting of N, C, O, P and S;

wherein Y is selected from the group consisting of O, N, S, P, C, —

O—

NH—

, —

O—

CH₂—

NH—

, —

O—

CH₂—

O—

, —

NH—

CH₂—

NH—

, —

O-CH(CH₃)—

NH—

, —

NH—

CH(CH₃)—

NH—

, —

O—

CH(CH₃)—

O—

, —

NH—

C(CH₃)₂—

NH—

, —

O—

S—

, —

O-CH₂—

S—

, —

NH—

S—

, —

NH—

CH₂—

S—

, and other mercaptan, phosphate, alkoxy, oxide, ether, esters (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;

with the proviso that if either X or Y is N, then the other is not C;

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇ and R₈ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups; and

wherein a, b, c, d, e, m, n and o are integers which may be the same or different and are independently selected from 0 to 2 for a, b, c, d, and e, and 0 to 5 for m, n and o.

2. The composition of claim 1, with the proviso that when q=1 and one of (R₁)_a, (R₂)_b, and (R₃)_c is oxygen and the other two are the same or different and are independently selected from the group consisting of hydrogen, methyl, ethyl and propyl, then A is not methyl, ethyl or propyl.

3. The composition of claim 1, wherein when a, b, or c is zero, the corresponding R group is a pair of electrons.

4. The composition of claim 1, wherein Y and/or X are N and m, n and o are 1.

5. The composition of claim 1, wherein Y and/or X are N and/or O, and m and n are 1, and o is 2.

6. The composition of claim 1, wherein said composition comprises at least two compounds having the formula I or II, or salts or esters thereof.

7. The composition of claim 6, wherein said composition comprises 2 to 5 compounds having the formula I or II, or salts or esters thereof.

8. The composition of claim 6, wherein said composition comprises an N-alkylimidazole compound.

9. The composition of claim 8, wherein said N-alkylimidazole compound is 1-methylimidazole or 4-methylimidazole.

10. The composition of claim 1, wherein said enzyme having nucleic acid polymerase activity is selected from the group consisting of a DNA polymerase, an RNA polymerase and a reverse transcriptase.

11. The composition of claim 10, wherein said DNA polymerase is selected from the group consisting of Taq, Tne, Tma, Pfu, VENT™

, DEEPVENT™ and

Tth DNA polymerases, and mutants and variants thereof.

12. The composition of claim 10, wherein said reverse transcriptase is selected from the group consisting of M-MLV reverse transcriptase, RSV reverse transcriptase, AMV reverse transcriptase, RAV reverse transcriptase, MAV reverse transcriptase and HIV reverse transcriptase, and mutants and variants thereof.

13. The composition of claim 10, wherein said reverse transcriptase is substantially reduced in RNase H activity.

14. A method for synthesizing a nucleic acid molecule, comprising:

(a) mixing a nucleic acid template with one or more of the compositions of claim 1 to form a mixture; and

(b) incubating said mixture under conditions whereby a first nucleic acid molecule complementary to all or a portion of said template is made.

15. The method of claim 14, further comprising incubating said first nucleic acid molecule under conditions whereby a second nucleic acid molecule complementary to all or a portion of said first nucleic acid molecule is made.

16. A nucleic acid molecule made according to the method of claim 14.

17. A method for amplifying a nucleic acid molecule comprising:

(a) mixing nucleic acid template with one or more of the compositions of claim 1 to form a mixture; and

(b) incubating said mixture under conditions whereby a nucleic acid molecule complementary to all or a portion of said template is amplified.

18. A method for sequencing a nucleic acid molecule comprising:

(a) mixing a nucleic acid molecule to be sequenced with one or more primers, one or more of the compositions of claim 1, one or more nucleotides and one or more terminating agents to form a mixture;

(b) incubating said mixture under conditions whereby a population of molecules complementary to all or a portion of said molecule to be sequenced is synthesized; and

(c) separating said population to determine the nucleotide sequence of all or a portion of said molecule to be sequenced.

19. A kit for use in synthesis of a nucleic acid molecule, said kit comprising one or more of the compositions of claim 1.

20. The kit of claim 19, wherein said kit comprises at least two of said compositions.

21. The kit of claim 19, further comprising one or more components selected from the group consisting of one or more nucleotides, one or more DNA polymerases, one or more reverse transcriptases, one or more suitable buffers, one or more primers and one or more terminating agents.

22. A composition for use in synthesizing a nucleic acid molecule, comprising one or more enzymes having polymerase activity and one or more compounds selected from the group consisting of 1-methylimidazole, 4-methylimidazole, 4-methylmorpholine N-oxide, poly(2-ethyl-2-oxazoline) of average molecular weight about 50,000 to about 500,000 daltons and poly(diallyldimethylamnmonium chloride) of average molecular weight about 100,000 to about 200,000 daltons.

23. The composition of claim 22, wherein said composition comprises at least two compounds selected from the group consisting of 1-methylimidazole, 4-methylimidazole, 4-methylmorpholine N-oxide, poly(2-ethyl-2-oxazoline) of average molecular weight about 50,000 to about 500,000 daltons and poly(diallyldimethylammonium chloride) of average molecular weight about 100,000 to about 200,000 daltons.

24. The composition of claim 22, wherein said enzyme having nucleic acid polymerase activity is selected from the group consisting of a DNA polymerase, an RNA polymerase and a reverse transcriptase.

25. The composition of claim 24, wherein said DNA polymerase is selected from the group consisting of Taq, Tne, Tma, Pfu, VENT™

, DEEPVENT™ and

Tth DNA polymerases, and mutants and variants thereof.

26. The composition of claim 24, wherein said reverse transcriptase is selected from the group consisting of M-MLV reverse transcriptase, RSV reverse transcriptase, AMV reverse transcriptase, RAV reverse transcriptase, MAV reverse transcriptase and HIV reverse transcriptase, and mutants and variants thereof.

27. The composition of claim 24, wherein said reverse transcriptase is substantially reduced in RNase H activity.

33. A method for synthesizing a nucleic acid molecule, comprising:

(a) mixing a nucleic acid template with one or more of the compositions of claim 22 to form a mixture; and

(b) incubating said mixture under conditions whereby a nucleic acid molecule complementary to all of a portion of said template is made.

34. The method of claim 33, wherein the bases of said nucleic acid template comprise greater than about 60% guanine and cytosine.

35. The method of claim 33, further comprising incubating said first nucleic acid molecule under conditions whereby a second nucleic acid molecule complementary to all or a portion of said first nucleic acid molecule is made.

36. A method for amplifying a nucleic acid molecule, comprising:

(a) mixing a nucleic template with one or more of the compositions of claim 22 to form a mixture; and

(b) incubating said mixture under conditions whereby a nucleic acid molecule complementary to all or a portion of said template is amplified.

37. The method of claim 36, wherein the bases of said nucleic acid template comprise greater than about 60% guanine and cytosine.

38. A method for sequencing a nucleic acid molecule, comprising:

(a) mixing a nucleic acid molecule to be sequenced with one or more primers, one or more of the compositions of claim 22, one or more nucleotides and one or more terminating agents to form a mixture;

(b) incubating said mixture under conditions whereby a population of molecules complementary to all or a portion of said molecules to be synthesized, is synthesized; and

(c) separating said population to determine the nucleotide sequence of all or a portion of said molecule to be sequenced.

39. The method of claim 38, wherein the bases of said nucleic acid template comprise greater than about 60% guanine and cytosine.

40. A kit for use in synthesis of a nucleic acid molecule, said kit comprising one or more of the compositions of claim 22.

41. The kit of claim 40, wherein said kit comprises at least two of said compositions.

42. The kit of claim 40, further comprising one or more components selected from the group consisting of one or more nucleotides, one or more DNA polymerases, one or more reverse transcriptases, one or more suitable buffers, one or more primers and one or more terminating agents.

28. A method for synthesizing a nucleic acid molecule, comprising:

(a) mixing a nucleic acid template with one or more compounds having a chemical formula selected from the group consisting of formula I or formula IL or a salt thereof, wherein said compound is not betaine;

Formula I;

where A is

where X is

where N is positively charged;

wherein q=1 to 100,000, wherein when q=2 to 100,000 each monomer of formula I may be the same as or different from the other monomers of formula I;

wherein Z may be the same as or different from Y;

wherein each Y and Z are independently selected from the group consisting of —

OH, —

NH₂, —

SH, —

PO₃H, —

CO₂H, —

SO₃H and hydrogen;

wherein f is an integer from 0 to 2, m is an integer from 0 to 20 and e is an integer from 0 to 2;

wherein R₄, R₅, and R₆ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, mercaptan, thiol, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups, and d is an integer from 0 to 2;

wherein a, b, and c are independently an integer from 0 to 1, with the proviso that no more than two of a, b, and c are zero;

wherein R₁, R₂ and R₃ may be the same or different and are independently selected from the group consisting of;

with the proviso that no more than two of A, R₁, R₂ and R₃ are selected from the group consisting of hydrogen, methyl, ethyl and propyl; and

with the proviso that if one, and only one, of R₁, R₂ and R₃ is ═

O, then A is none of hydrogen, methyl, ethyl and propyl;

wherein each R₇ and W may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups;

g is an integer from 0 to 2 and n is an integer from 0 to 20, with the proviso that if two of R₁, R₂, and R₃ are ═

O, then the other is not ═

O;

Formula II;

wherein Formula II is saturated or unsaturated;

wherein q=1 to 100,000, wherein when q=2 to 100,000, each monomer of formula II may be the same as or different from each other monomer of formula II;

wherein X is selected from the group consisting of N, C, O, P and S;

wherein Y is selected from the group consisting of O, N, S, P, C, —

O—

NH—

, —

O—

CH₂—

NH—

, —

O—

CH₂—

O—

, —

NH—

CH₂—

NH—

, —

O—

CH(CH₃)—

NH—

, —

NH—

CH(CH₃)—

NH—

, —

O—

CH(CH₃)—

O—

, —

NH—

C(CH₃)₂—

NH—

, —

O—

S—

, —

O—

CH₂—

S—

, —

NH—

S—

, —

NH—

CH₂—

S—

, and other mercaptan, phosphate, alkoxy, oxide, ether, esters (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;

with the proviso that if either X or Y is N, then the other is not C;

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇ and R₈ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups; and

wherein a, b, c, d, e, m, n and o are integers which may be the same or different and are independently selected from 0 to 2 for a, b, c, d, and e, and 0 to 5 for m, n and o, to form a mixture; and

(b) incubating said mixture under conditions whereby a first nucleic acid molecule complementary to all or a portion of said template is made, wherein the bases of said nucleic acid template comprise greater than about 60% guanine and cytosine.

29. The method of claim 28, further comprising incubating said first nucleic acid molecule under conditions whereby a second nucleic acid molecule complementary to all or a portion of said first nucleic acid molecule is made.

30. A nucleic acid molecule made according to the method of claim 28.

31. A method for amplifying a nucleic acid molecule, comprising:

(a) mixing a nucleic acid template with one or more compounds having a chemical formula selected from the group consisting of formula I or formula II, or a salt thereof, wherein said compound is not betaine;

Formula I;

where A is

where X is

where N is positively charged;

wherein q=1 to 100,000, wherein when q=2 to 100,000 each monomer of formula I may be the same as or different from the other monomers of formula II;

wherein Z may be the same as or different from Y;

wherein each Y and Z are independently selected from the group consisting of —

OH, —

NH₂, —

SH, —

PO₃H, —

CO₂H, —

SO₃H and hydrogen;

wherein f is an integer from 0 to 2, m is an integer from 0 to 20 and e is an integer from 0 to 2;

wherein R₄, R₅, and R₆ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, mercaptan, thiol, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups, and d is an integer from 0 to 2;

wherein a, b, and c are independently an integer from 0 to 1, with the proviso that no more than two of a, b, and c are zero;

wherein R₁, R₂ and R₃ may be the same or different and are independently selected from the group consisting of;

with the proviso that no more than two of A, R₁, R₂ and R₃ are selected from the group consisting of hydrogen, methyl, ethyl and propyl; and

with the proviso that if one, and only one, of R₁, R₂ and R₃ is ═

O, then A is none of hydrogen, methyl, ethyl and propyl;

wherein each R₇ and W may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amnino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups;

g is an integer from 0 to 2 and n is an integer from 0 to 20, with the proviso that if two of R₁, R₂, and R₃ are ═

O, then the other is not ═

O;

Formula II;

wherein Formula II is saturated or unsaturated;

wherein q=1 to 100,000, wherein when q=2 to 100,000, each monomer of formula II may be the same as or different from each other monomer of formula II;

wherein X is selected from the group consisting of N, C, O, P and S;

wherein Y is selected from the group consisting of O, N, S, P, C, —

O—

NH—

, —

O—

CH₂—

NH—

, —

O—

CH₂—

O—

, —

NH—

CH₂—

NH—

, —

O—

CH(CH₃NH—

, —

NH—

CH(CH₃)—

NH—

, —

O—

CH(CH₃)—

O—

, —

NH—

C(CH₃)₂—

NH—

, —

O—

S—

, —

O—

CH₂—

S—

, —

NH—

S—

, —

NH—

CH₂—

S—

, and other mercaptan, phosphato, alkoxy, oxide, ether, esters (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;

with the proviso that if either X or Y is N, then the other is not C;

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇ and R₈ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups; and

wherein a, b, c, d, e, m, n and o are integers which may be the same or different and are independently selected from 0 to 2 for a, b, c, d, and e, and 0 to 5 for m, n and o, to form a mixture; and

(b) incubating said mixture under conditions whereby a nucleic acid molecule complementary to all or a portion of said template is amplified, wherein the bases of said nucleic acid template comprise greater than about 60% guanine and cytosine.

32. A method for sequencing a nucleic acid molecule, comprising:

(a) mixing a nucleic acid molecule to be sequenced with one or more primers, one or more compounds having a chemical formula selected from the group consisting of formula I or formula II, or a salt thereof, wherein said compound is not betaine;

Formula I;

where A is

where X is

where N is positively charged;

wherein q=1 to 100,000, wherein when q=2 to 100,000 each monomer of formula I may be the same as or different from the other monomers of formula I;

wherein Z may be the same as or different from Y;

wherein each Y and Z are independently selected from the group consisting of —

OH, —

NH_2,—

SH, —

PO₃H, —

CO₂H, —

SO₃H and hydrogen;

wherein f is an integer from 0 to 2, m is an integer from 0 to 20 and e is an integer from 0 to 2;

wherein R₄, R₅, and R₆ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, mercaptan, thiol, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups, and d is an integer from 0 to 2;

wherein a, b, and c are independently an integer from 0 to 1, with the proviso that no more than two of a, b, and c are zero;

wherein R₁, R₂ and R₃ may be the same or different and are independently selected from the group consisting of;

with the proviso that no more than two of A, R₁, R₂ and R₃ are selected from the group consisting of hydrogen, methyl, ethyl and propyl; and

with the proviso that if one, and only one, of R₁, R₂ and R₃ is ═

O, then A is none of hydrogen, methyl, ethyl and propyl;

wherein each R₇ and W may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, carbonyl, sulfonyl, sulfonic and amido groups;

g is an integer from 0 to 2 and n is an integer from 0 to 20, with the proviso that if two of R₁, R₂, and R₃ are ═

O, then the other is not ═

O;

Formula II;

wherein Formula II is saturated or unsaturated;

wherein q=1 to 100,000, wherein when q=2 to 100,000, each monomer of formula II may be the same as or different from each other monomer of formula II;

wherein X is selected from the group consisting of N, C, O, P and S;

wherein Y is selected from the group consisting of O, N, S, P, C,—

O—

NH—

, —

O—

CH₂—

NH—

, —

O—

CH₂—

O—

, —

NH—

CH₂—

NH—

, —

O—

CH(CH₃)NH—

, —

NH—

CH(CH₃)—

NH—

, —

O—

CH(CH₃)—

O—

, —

NH—

C(CH₃)₂—

NH—

, —

O—

S—

, —

O—

CH₂—

S—

, —

NH—

S—

, —

NH—

CH₂—

S—

, and other mercaptan, phosphate, alkoxy, oxide, ether, esters (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups;

with the proviso that if either X or Y is N, then the other is not C;

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇ and R₈ may be the same or different and are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, aryl, amino, thiol, mercaptan, halo, nitro, nitrilo, hydroxy, hydroxyalkyl, hydroxyaryl, phosphato, alkoxy, oxide, ether, ester (alkanoyloxy), carboxy, sulfonyl, sulfonic and amido groups; and

wherein a, b, c, d, e, m, n and o are integers which may be the same or different and are independently selected from 0 to 2 for a, b, c, d, and e, and 0 to 5 for m, n and o, one or more nucleotides and one or more terminating agents to form a mixture;

(b) incubating said mixture under conditions whereby a population of molecules complementary to all or a portion of said molecule to be sequenced is synthesized; and

(c) separating said population to determine the nucleotide sequence of all or a portion of said molecule to be sequenced, wherein the bases of said nucleic acid molecule to be sequenced comprise greater than about 60% guanine and cytosine.