Bisulfite conversion of DNA

1. Use of a compound for the bisulfite conversion of DNA, said use comprising converting isolated genomic DNA in the presence of the compound, wherein the compound has the following formula:

wherein R 1 is selected from the group consisting of

a) H;

b) COOH; and

c) [CH 2 CH 2 CH 2 (CH 3 )] 3 —CH 3 ;

wherein R 2 is selected from the group consisting of

a) H;

b) OH; and

c) OAc; and

wherein the isolated genomic DNA is in a solution containing bisulfite and a denaturing agent or is denatured in a solution containing bisulfite;

whereby the DNA is bisulfite converted.

2. The use according to claim 1 , wherein the concentration of the compound is between 35 and 50 mmol/l.

3. The use according to claim 1 , wherein the DNA is derived from body fluid.

4. The use according to claim 1 , wherein the body fluid is serum or plasma.

5. The use according to claim 1 , wherein the DNA is derived from tissue, sputum, stool, urine, or cerebrospinal fluid.

6. The use according to claim 1 , further comprising analyzing the converted DNA by amplification of the DNA by a method selected from the group consisting of:

a) a method using methylation-specific blockers;

b) a method using methylation-sensitive PCR;

c) a method using primer extension reactions;

d) a method using hybridization of oligomer arrays; and

e) a method using real time PCR.

7. The use according to claim 1 , wherein the compound is 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid.

8. Use of a compound for the bisulfite conversion of DNA, said use comprising converting isolated genomic DNA in the presence of the compound, wherein the compound has the following formula:

wherein R is selected from the group consisting of

a) H;

b) COOH; and

c) [CH 2 CH 2 CH 2 (CH 3 )] 3 —CH 3 ; and

wherein the isolated genomic DNA is in a solution containing bisulfite and a denaturing agent or is denatured in a solution containing bisulfite;

whereby the DNA is bisulfite converted.

9. The use according to claim 8 , wherein the concentration of the compound is between 35 and 50 mmol/l.

10. The use according to claim 8 , wherein the DNA is derived from body fluid.

11. The use according to claim 8 , wherein the body fluid is serum or plasma.

12. The use according to claim 8 , wherein the DNA is derived from tissue, sputum, stool, urine, or cerebrospinal fluid.

13. The use according to claim 8 , comprising analyzing the converted DNA by amplification of the DNA by a method selected from the group consisting of:

a) a method using methylation-specific blockers;

b) a method using methylation-sensitive PCR;

c) a method using primer extension reactions;

d) a method using hybridization of oligomer arrays; and

e) a method using real time PCR.

14. Use of a compound for the bisulfite conversion of DNA, said use comprising converting isolated genomic DNA in the presence of the compound, wherein the compound has the following formula:

wherein the isolated genomic DNA is in a solution containing bisulfite and a denaturing agent or is denatured in a solution containing bisulfite;

whereby the DNA is bisulfite converted.

15. The use according to claim 14 , wherein the concentration of the compound is between 35 and 50 mmol/l.

16. The use according to claim 14 , wherein the DNA is derived from body fluid.

17. The use according to claim 14 , wherein the body fluid is serum or plasma.

18. The use according to claim 14 , wherein the DNA is derived from tissue, sputum, stool, urine, or cerebrospinal fluid.

19. The use according to claim 14 , comprising analyzing the converted DNA by amplification of the DNA by a method selected from the group consisting of:

a) a method using methylation-specific blockers;

b) a method using methylation-sensitive PCR;

c) a method using primer extension reactions;

d) a method using hybridization of oligomer arrays; and

e) a method using real time PCR.

20. A method for the bisulfite conversion of DNA, wherein the method is conducted in the presence of a radical scavenger having the following formula:

wherein R 1 is selected from the group consisting of

a) H;

b) COOH; and

C) [CH 2 CH 2 CH 2 (CH 3 )] 3 —CH 3 ;

wherein R 2 is selected from the group consisting of

a) H;

b) OH; and

c) OAc; and

wherein the DNA is isolated genomic DNA in a solution containing bisulfite and a denaturing agent or is denatured in a solution containing bisulfite;

whereby the DNA is bisulfite converted.

21. The method according to claim 20 , further comprising analyzing the converted DNA by amplification of the DNA by a method selected from the group consisting of:

a) a method using methylation-specific blockers;

b) a method using methylation-sensitive PCR;

c) a method using primer extension reactions;

d) a method using hybridization of oligomer arrays; and

e) a method using real time PCR.

22. The method according to claim 20 , wherein the compound is 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid.

23. The method according to claim 20 , wherein the bisulfite conversion is conducted at greater than 50° C. for greater than or equal to 5 hours.

24. The method according to claim 20 , wherein the bisulfite conversion is conducted at a temperature of >55° C.

25. The method according to claim 20 , wherein the bisulfite conversion is conducted at a temperature of 60° C. for 5 hours or at a temperature of 55° C. for 7 hours.

26. The method according to claim 20 , wherein the DNA is derived from bodily fluid.

27. The method according to claim 26 , wherein the bodily fluid is blood or plasma.

28. The method according to claim 20 , wherein the bisulfite conversion is carried out in the presence of dioxane, a dioxane derivative, or a similar aliphatic cyclic ether.

29. The method according to claim 20 , wherein the bisulfite conversion is carried out in the absence of denaturing solvents or reagents.

30. The method according to claim 20 , wherein the reaction temperature is increased to a range of between 85° C. and 100° C. briefly during the course of the conversion.

31. The method according to claim 20 , wherein the converted DNA is purified by a means of ultrafiltration.

32. A method for the bisulfite conversion of DNA, wherein the method is conducted in the presence of a radical scavenger having the following formula:

wherein R is selected from the group consisting of

a) H;

b) COOH; and

c) [CH 2 CH 2 CH 2 (CH 3 )] 3 —CH 3 ; and

wherein the isolated genomic DNA is in a solution containing bisulfite and a denaturing agent or is denatured in a solution containing bisulfite;

whereby the DNA is bisulfite converted.

33. The method according to claim 32 , further comprising analyzing the converted DNA by amplification of the DNA by a method selected from the group consisting of:

a) a method using methylation-specific blockers;

b) a method using methylation-sensitive PCR;

c) a method using primer extension reactions;

d) a method using hybridization of oligomer arrays; and

e) a method using real time PCR.

34. The method according to claim 32 , wherein the bisulfite conversion is conducted at greater than 50° C. for greater than or equal to 5 hours.

35. A method for the bisulfite conversion of DNA, wherein the method is conducted in the presence of a radical scavenger having the following formula:

wherein the isolated genomic DNA is in a solution containing bisulfite and a denaturing agent or is denatured in a solution containing bisulfite;

whereby the DNA is bisulfite converted.

36. The method according to claim 35 , further comprising analyzing the converted DNA by amplification of the DNA by a method selected from the group consisting of:

a) a method using methylation-specific blockers;

b) a method using methylation-sensitive PCR;

c) a method using primer extension reactions;

d) a method using hybridization of oligomer arrays; and

e) a method using real time PCR.

37. The method according to claim 35 , wherein the bisulfite conversion is conducted at greater than 50° C. for greater than or equal to 5 hours.