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PMID: 9520387 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Transcriptional sequencing: A method for DNA sequencing using RNA polymerase.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 95 ·No. 7 ·1998-03-31 ·Pages 3455-60

Sasaki N, Izawa M, Watahiki M, Ozawa K, Tanaka T, Yoneda Y, Matsuura S, Carninci P, Muramatsu M, Okazaki Y, Hayashizaki Y

Abstract

We have developed a sequencing method based on the RNA polymerase chain termination reaction with rhodamine dye attached to 3'-deoxynucleoside triphosphate (3'-dNTP). This method enables us to conduct a rapid isothermal sequencing reaction in <30 min, to reduce the amount of template required, and to do PCR direct sequencing without the elimination of primers and 2'-dNTP, which disturbs the Sanger sequencing reaction. An accurate and longer read length was made possible by newly designed four-color dye-3'-dNTPs and mutated RNA polymerase with an improved incorporation rate of 3'-dNTP. This method should be useful for large-scale sequencing in genome projects and clinical diagnosis.

MeSH Terms

DNA/genetics DNA, Fungal/genetics DNA-Directed RNA Polymerases/genetics Genome Saccharomyces cerevisiae/genetics Sequence Analysis, DNA/methods Transcription, Genetic

Chemicals

DNA, Fungal DNA DNA-Directed RNA Polymerases

Authors & Affiliations

11 authors, click to expand affiliations / ORCID

Sasaki N

Genome Science Laboratory, Tsukuba Life Science Center, The Institute of Physical and Chemical Research, 3-1-1 Koyadai, Tsukuba, Ibaraki 305, Japan.

Izawa M

Watahiki M

Ozawa K

Tanaka T

Yoneda Y

Matsuura S

Carninci P

Muramatsu M

Okazaki Y

Hayashizaki Y

References (24)

24 references, click to expand

DNA sequence analysis with a modified bacteriophage T7 DNA polymerase.
Proc Natl Acad Sci U S A. 1987 Jul;84(14):4767-71 PMID: 3474623
Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP.
Nucleic Acids Res. 1986 Feb 11;14(3):1319-24 PMID: 3951988
Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.
Science. 1988 Jan 29;239(4839):487-91 PMID: 2448875
DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA.
Proc Natl Acad Sci U S A. 1988 Dec;85(24):9436-40 PMID: 3200828
Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension.
Gene. 1989 Apr 15;77(1):61-8 PMID: 2744488
DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Effect of pyrophosphorolysis and metal ions.
J Biol Chem. 1990 May 15;265(14):8322-8 PMID: 2159476
Identification of a region of the bacteriophage T3 and T7 RNA polymerases that determines promoter specificity.
J Mol Biol. 1990 Sep 5;215(1):31-9 PMID: 2204707
Use of inorganic pyrophosphatase to improve the yield of in vitro transcription reactions catalyzed by T7 RNA polymerase.
Biotechniques. 1990 Dec;9(6):713-4 PMID: 1702976
Rapid and simple purification of T7 RNA polymerase.
Nucleic Acids Res. 1991 Apr 25;19(8):1948 PMID: 2030975
Aberrations of the tumor suppressor p53 and retinoblastoma genes in human hepatocellular carcinomas.
Cancer Res. 1991 Oct 15;51(20):5520-5 PMID: 1655254
Screening for mutations by RNA single-strand conformation polymorphism (rSSCP): comparison with DNA-SSCP.
Nucleic Acids Res. 1992 Feb 25;20(4):871-8 PMID: 1371869
DNA sequencing with dye-labeled terminators and T7 DNA polymerase: effect of dyes and dNTPs on incorporation of dye-terminators and probability analysis of termination fragments.
Nucleic Acids Res. 1992 May 25;20(10):2471-83 PMID: 1598205
DNA sequencing using capillary array electrophoresis.
Anal Chem. 1992 Sep 15;64(18):2149-54 PMID: 1416049
Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution.
Nature. 1993 Aug 12;364(6438):593-9 PMID: 7688864
Direct sequencing of PCR products in agarose gel slices.
Nucleic Acids Res. 1994 Aug 25;22(16):3425-6 PMID: 7915835
Convenient single-step, one tube purification of PCR products for direct sequencing.
Nucleic Acids Res. 1994 Oct 11;22(20):4354-5 PMID: 7937169
Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis.
Proc Natl Acad Sci U S A. 1995 May 9;92(10):4347-51 PMID: 7753809
A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides.
Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6339-43 PMID: 7603992
How is the Human Genome Project doing, and what have we learned so far?
Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10841-8 PMID: 7479895
Transcribing of Escherichia coli genes with mutant T7 RNA polymerases: stability of lacZ mRNA inversely correlates with polymerase speed.
Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12250-4 PMID: 8618879
Microfabrication technologies for integrated nucleic acid analysis.
Genome Res. 1997 Mar;7(3):189-97 PMID: 9074923
Molecular cloning of the human thyrotropin-beta subunit gene.
FEBS Lett. 1985 Sep 2;188(2):394-400 PMID: 3839756
Transcription from bacteriophage T7 and SP6 RNA polymerase promoters in the presence of 3'-deoxyribonucleoside 5'-triphosphate chain terminators.
Biochemistry. 1985 Oct 8;24(21):5716-23 PMID: 3002422
A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides.
Science. 1987 Oct 16;238(4825):336-41 PMID: 2443975

Article Info

Journal

Proceedings of the National Academy of Sciences of the United States of America

Abbr.

Proc Natl Acad Sci U S A

ISSN

0027-8424

DOI

10.1073/pnas.95.7.3455

Published

1998-03-31

Pages

3455-60

Language

English

Region

United States

NLM ID

7505876

PMCID

PMC19857

Subset

External Links

PubMed source DOI: 10.1073/pnas.95.7.3455 PMC Full Text View journal details

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