Method for producing double-stranded DNA whose terminal homopolymer part is eliminated and method for determining nucleotide sequence

• US 6,344,345 B1
• Filed: 11/05/1999
• Issued: 02/05/2002
• Est. Priority Date: 11/06/1998
• Status: Expired due to Term

• Current Assignee: Kabushiki Kaisha Dnaform, Riken
• Original Assignee: Riken
• Inventors: Hayashizaki, Yoshihide
• Primary Examiner(s): Whisenant, Ethan
• Assistant Examiner(s): LU, FRANK WEI MIN
• Application Number:
  US09/434,131
• Time in Patent Office: 823 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/91.51, 435/320.1, 435/183, 436/94, 536/23.1, 536/24.3, 536/24.33, 536/25.3
• US Class Current: 435/91.1
• CPC Class Codes: C12N 15/1096 cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Disclosed is a method for producing double-stranded DNA comprising treating double-stranded DNA having a homopolymer part or parts at one or both ends with a restriction enzyme to partly or fully eliminate at least one of the homopolymer part or parts. The restriction enzyme is capable of cleaving double-stranded DNA at a cleavage site separate from a recognition site therefor. Disclosed is a method for determining a nucleotide sequence of double-stranded DNA utilizing one or both strands of the double-stranded DNA as a template, wherein the double-stranded DNA used as the template is double-stranded DNA prepared by the above method of the present invention. The present invention provides a method for producing double-stranded DNA a part or all of which homopolymer part, which may inhibit nucleotide sequence determination, is eliminated, and a method for determining a nucleotide sequence utilizing as a template the double-stranded DNA prepared by the above method of the present invention, whose homopolymer part is partially or fully eliminated.

Claims

1. A method for producing double-stranded DNA comprising:

providing single-stranded DNA comprising a homopolymer at one or both ends;

employing said single-stranded DNA to produce a double-stranded DNA comprising a homopolymer at one or both ends;

wherein the double-stranded DNA does not contain internal type IIS restriction sites or is chemically modified in order to protect the double-stranded DNA from internal type IIS restriction enzyme cleavage;

after producing said double-stranded DNA, treating said double-stranded DNA comprising a homopolymer at one or both ends with a type IIS restriction enzyme to partly or fully eliminate at least one of the homopolymers, wherein the restriction enzyme is capable of cleaving said double-stranded DNA at a cleavage site separate from the recognition site therefor.

2. The method according to claim 1, wherein the double stranded DNA is double-stranded cDNA.

3. The method according to claim 1, wherein the double-stranded DNA is hemimethylated double-stranded cDNA or chemically synthesized double-stranded DNA.

4. The method according to claim 1, wherein the end(s) of the double-stranded DNA comprise(s) both a homopolymer and a non-homopolymer, and at least a portion of the non-homopolymer constitutes the recognition site for the restriction enzyme.

5. The method according to claim 1, wherein the homopolymer contained in the double-stranded DNA is an oligo dG:

dC pair or an oligo dA;

dT pair.

6. The method according to claim 1, wherein the class IIS restriction enzyme is selected from the group consisting of AlwI, AlwXI, Alw26I, BbsI, BbvI, BbvII, BcefI, BccI, BcgI, BciVI, BinI, BmrI, BpmI, BsaI, BseRI, BsgI, BsmAI, BsmBI, BspMI, BsrDI, BstF5I, EarI, Eco31I, Eco57I, Esp3I, Faul, FokI, GsuI, HgaI, HinGUII, HphI, Ksp632I, MboII, MmeI, MnI1I, NgoVIII, PleI, RleAI, SapI, SfaNI, TaqII, Tth11II BsmI, BsrI, BsmFI and BseMII.

7. The method according to claim 1, wherein the double-stranded DNA is hemimethylated in a part of one strand other than the homopolymer.

8. The method according to claim 7, wherein the hemimethylation is introduced into cytosine or adenine.

9. The method according to claim 7, wherein the restriction enzyme is a restriction enzyme that does not act on double-stranded DNA that is hemimethylated at the recognition site or the cleavage site.

10. The method according to claim 9, wherein the restriction enzyme is a restriction enzyme that does not act on double-stranded DNA having a methyl group as the chemical modification.

11. The method according to claim 10, wherein the restriction enzyme is BbvI, HgaI or GsuI.

12. A method for determining a nucleotide sequence of double-stranded DNA utilizing one or both strands of the double-stranded DNA as a template, wherein the double-stranded DNA used as the template is double-stranded DNA prepared by the method according to claim 1.

13. The method according to claim 12, wherein the prepared double-stranded DNA is amplified by PCR or by using a microorganism, and the nucleotide sequence determination is performed by using the amplified double-stranded DNA as the template.

14. The method according to claim 12, wherein oligo dG:

dC of the prepared double-stranded DNA has been partly or fully eliminated.

15. The method according to claim 13, wherein oligo dG:

dC of the prepared double-stranded DNA has been partly or fully eliminated.

16. The method according to claim 12, wherein the nucleotide sequence determination is performed by forming a nucleic acid transcript of the double-stranded DNA in the presence of a terminator for nucleic acid transcription, and analyzing the resulting nucleic acid transcript.

17. The method according to claim 13, wherein the nucleotide sequence determination is performed by forming a nucleic acid transcript of the double-stranded DNA in the presence of a terminator for nucleic acid transcription, and analyzing the resulting nucleic acid transcript.

18. The method according to claim 16, wherein the nucleic acid transcription is performed by using an RNA polymerase.

19. The method according to claim 17, as wherein the nucleic acid transcription is performed by using an RNA polymerase.