Nucleic acid sequence analysis with nucleoside-5'-O-(1-thiotriphosphates)

• US 5,187,085 A
• Filed: 09/28/1990
• Issued: 02/16/1993
• Est. Priority Date: 09/28/1990
• Status: Expired due to Term

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lee, Linda G.
• Primary Examiner(s): YARBROUGH, AMELIA
• Application Number:
  US07/590,218
• Time in Patent Office: 872 Days
• Field of Search: 435/6, 435/91, 435/172.3, 435/968, 436/501, 436/800, 436/811, 935/78, 935/88
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/113 incorporating modified backbone
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: Y10S 435/968 High energy substrates, e.g. fluorescent, chemiluminescent, radioactive
• CPC Class Codes: Y10S 436/80 Fluorescent dyes, e.g. rhodamine

Abstract

A chain-termination method of nucleic acid sequence determination is provided wherein nucleoside triphosphate precursors are replaced with their 1-thiotriphosphate analogs in the polymerization step. This substitution results in more uniform bands of electrophoretically separated DNA fragments which, in turn, results in more accurate base determination.

Claims

1. A method of determining the nucleotide sequence of a target nucleic acid, the method comprising the steps of:

providing a template nucleic acid, the template nucleic acid containing the target nucleic acid;

providing an oligonucleotide primer for the template nucleic acid;

hybridizing the oligonucleotide primer to the template nucleic acid;

extending the oligonucleotide primer with a nucleic acid polymerase in a reaction mixture comprising nucleotide precursors and at least one chain-terminating nucleotide to form a nested series of DNA fragment populations such that every DNA fragment of the same size terminates with the same chain-terminating nucleotide, wherein said nucleotide precursors consist of nucleoside-5'"'"'-O-(1-thiotriphosphate)s;

separating the DNA fragment populations by size; and

identifying the chain-terminating nucleotide associated with each DNA fragment population.

2. The method of claim 1 wherein said step of separating includes separating said DNA fragment populations by gel electrophoresis to form bands of DNA fragment populations such that each band corresponds to DNA fragments of the same size.

3. The method of claim 2 wherein said at least one chain-terminating nucleotide consists of dideoxyadenosine labelled with a first dye, dideoxycytidine labelled with a second dye, dideoxyguansine labelled with a third dye, and dideoxythymidine labelled with a fourth dye, the first, second, third, and fourth dyes being spectrally resolvable with respect to one another, and wherein said step of identifying includes the steps of illuminating said bands of DNA fragments so that the first, second, third, and fourth dyes are caused to fluoresce, and measuring the fluorescence and/or absorption characteristic of the first, second, third, and fourth dyes.

4. The method of claim 3 wherein said nucleic acid polymerase is Sequenase.

5. The method of claim 4 wherein said dideoxyadenosine is 2'"'"',3'"'"'-dideoxy-7-deazaadenosine and said first dye is attached by way of a linking group to a 7 carbon atom thereof;

said dideoxycytidine is 2'"'"',3'"'"'-dideoxycytidine and said second dye is attached by way of a linking group to a 5 carbon atom thereof;

said dideoxyguanosine is selected from the group consisting of 2'"'"',3'"'"'-dideoxy-7-deazaguanosine and 2'"'"',3'"'"'-dideoxy-7-deazainosine and said third dye is attached by way of a linking group to a 7 carbon atom thereof; and

said dideoxythymidine is 2'"'"',3'"'"'-dideoxyuridine and said fourth dye is attached by way of a linking group to a 5 carbon atom thereof.

6. The method of claim 5 wherein said first, second, third, and fourth dyes are selected from the group consisting of rhodamine dyes and fluorescein dyes.

7. The method of claim 6 wherein said linking group is 3-carboxyamino-1-propynyl and links said 7 carbon atoms of said 2'"'"',3'"'"'-dideoxy-7-deazaadenosine and said dideoxyguanosine selected from the group consisting of 2'"'"',3'"'"'-dideoxy-7-deazaguanosine and 2'"'"',3'"'"'-dideoxy-7-deazainosine to a 5 or 6 carbon atom of said first and third dyes, respectively, and links said 5 carbon atoms of said dideoxycytidine and said dideoxythymidine to a 5 or 6 carbon atom of said second and fourth dyes, respectively.

8. The method of claim 7 wherein said first, second, third, and fourth dyes are selected from the group consisting of rhodamine X, tetramethylrhodamine, rhodamine 110, and rhodamine 6G.

9. The method of claim 8 wherein said 2'"'"',3'"'"'-dideoxy-7-deazaadenosine is attached to said 5 carbon atom of rhodamine 6G, said 2'"'"',3'"'"'-dideoxycytidine is attached to said 6 carbon atom of rhodamine X, said dideoxyguanosine selected from the group consisting of 2'"'"',3'"'"'-dideoxy-7-deazaguanosine and 2'"'"',3'"'"'-dideoxy-7-deazainosine is attached to said 5 carbon atom of rhodamine 110, and said 2'"'"',3'"'"'-dideoxyuridine is attached to said 6 carbon atom of tetramethylrhodamine.

10. The method of claim 7 wherein said first, second, third, fourth dyes are selected from the group consisting of 5-(and 6-)carboxyfluorescein, 2'"'"',7'"'"'-dichloro-5-(and 6-)carboxyfluorescein, 2'"'"',7'"'"'-dimethoxy-4'"'"',5'"'"'-dichloro-5-(and 6-)carboxy-4,7-dichlorofluorescein, and 1'"'"',2'"'"',7'"'"',8'"'"'-dibenzo-5-(and 6-)carboxy-4.7-dichlorofluorescein.

11. The method of claim 10 wherein said 2'"'"',3'"'"'-dideoxy-7-deazaadenosine is attached to said 5 carbon atoms of 2'"'"',7'"'"'-dimethoxy-4'"'"',5'"'"'-dichloro-4,7-dichlorofluorescein, said 2'"'"',3'"'"'-dideoxycytidine is attached to said 5 carbon atom of 2'"'"',7'"'"'-dichlorofluorescein, said dideoxyguanosine selected from the group consisting of 2'"'"',3'"'"'-dideoxy-7-deazaguanosine and 2'"'"',3'"'"'-dideoxy-7-deazainosine is attached to said 5 carbon atom of 1'"'"',2'"'"',7'"'"',8'"'"'-dibenzo-4,7-dichlorofluorescein, and said 2'"'"',3'"'"'-dideoxyuridine is attached to said 6 carbon atom of fluorescein.

12. The method of claim 1 wherein said steps of providing said template nucleic acid, providing said oligonucleotide primer, hybridizing, and extending include providing an oligonucleotide primer for said template nucleic acid in each of four separate reaction mixtures and separates extending the oligonucleotide primers to form four nested series of DNA fragment populations.

13. The method of claim 12 wherein said DNA fragment populations are radioactively labelled, and wherein said step of separating includes separating by gel electrophoresis each of said four DNA fragment populations to form separate sets of bands of DNA fragment populations such that each band corresponds to DNA fragments of the same size.

14. The method of claim 12 wherein each of said oligonucleotide primers has a label.

15. The method of claim 14 wherein said label for each of said oligonucleotide primers is different.

16. The method of claim 15 wherein said label is selected from a set of spectrally resolvable fluorescent dyes.

17. In a method of determining the nucleotide sequence of a target nucleic acid, the method of the type wherein a nested series of DNA fragment populations is generated by extending an oligonucleotide primer with a nucleic acid polymerase in the presence of one or more chain-terminating nucleotides and wherein the nested series of DNA fragment populations is separated by size, an improvement comprising:

extending the oligonucleotide primer with the nucleic acid polymerase in a reaction mixture comprising nucleotide precursors consisting of nucleoside-5'"'"'-O-(1-thiotriphosphate)s.

18. The method of claim 17 wherein said DNA fragment populations are separated by gel electrophoresis.

19. The method of claim 18 wherein said one or more chain-terminating nucleotides consist of dideoxyadenosine labelled with a first fluorescent dye, dideoxycytidine labelled with a second fluorescent dye, dideoxyguanosine labelled with a third fluorescent dye, and dideoxythymidine labelled with a fourth fluorescent dye, the first, second, third, and fourth fluorescent dyes being spectrally resolvable with respect to one another.

20. The method of claim 19 wherein said nucleic acid polymerase is Sequenase.