Recognition sites of eukaryotic DNA topoisomerase I: DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA

Kenneth A. Edwards, Brian D. Halligan, John L. Davis, Nadine L. Nivera, Leroy-Fong Liu

Research output: Contribution to journalArticle

90 Citations (Scopus)

Abstract

Eukaryotic DNA topoisomerase I introduces transient single-stranded breaks on double-stranded DNA and spontaneously breaks down single-stranded DNA. The cleavage sites on both single and double-stranded SV40 DNA have been determined by DNA sequencing. Consistent with other reports, the eukaryotic enzymes, in contrast to prokaryotic type I topoisomerases, links to the 3'-end of the cleaved DNA and generates a free 5'-hydroxyl end on the other half of the broken DNA strand. Both human and calf enzymes cleave SV40 DNA at identical and specific sites. From 827 nucleotides sequenced, 68 cleavage sites were mapped. The majority of the cleavage sites were present on both double and single-stranded DNA at exactly the sane nucleotide positions, suggesting that the DNA sequence is essential for enzyme recognition. By analyzing all the cleavage sequences, certain nucleotides are found to be less favored at the cleavage sites. There is a high probability to exclude G from positions -4, -2, -1 and +1, T from position -3, and A from position -1. These five positions(-4 to +1 oriented in the 5' to 3' direction) around the cleavage sites must interact intimately with topo I and thus are essential for enzyme recognition. One topo I cleavage site which shows an atypical cleavage sequence maps in the middle of a palindromic sequence near the origin of SV40 DNA replication. It occurs only on single-stranded SV40 DNA, suggesting that the DNA hairpin can alter the cleavage specificity. The strongest cleavage site maps near the origin of SV40 DNA replication at nucleotide 31-32 and has a pentanucleotide sequence of 5'-TGACT-3'.

Original languageEnglish
Pages (from-to)2565-2576
Number of pages12
JournalNucleic Acids Research
Volume10
Issue number8
DOIs
Publication statusPublished - Apr 24 1982
Externally publishedYes

Fingerprint

Type I DNA Topoisomerase
Nucleotides
DNA Sequence Analysis
Sequencing
DNA
Enzymes
Single-Stranded DNA
DNA Replication
DNA Sequencing
Double-Stranded DNA Breaks
DNA Sequence
Specificity
Breakdown
Hydroxyl Radical
DNA sequences
Replication

ASJC Scopus subject areas

  • Statistics, Probability and Uncertainty
  • Applied Mathematics
  • Health, Toxicology and Mutagenesis
  • Toxicology
  • Genetics(clinical)
  • Genetics

Cite this

Recognition sites of eukaryotic DNA topoisomerase I : DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA. / Edwards, Kenneth A.; Halligan, Brian D.; Davis, John L.; Nivera, Nadine L.; Liu, Leroy-Fong.

In: Nucleic Acids Research, Vol. 10, No. 8, 24.04.1982, p. 2565-2576.

Research output: Contribution to journalArticle

Edwards, Kenneth A. ; Halligan, Brian D. ; Davis, John L. ; Nivera, Nadine L. ; Liu, Leroy-Fong. / Recognition sites of eukaryotic DNA topoisomerase I : DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA. In: Nucleic Acids Research. 1982 ; Vol. 10, No. 8. pp. 2565-2576.
@article{00892c2c736e47cda7d917fc991e53d9,
title = "Recognition sites of eukaryotic DNA topoisomerase I: DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA",
abstract = "Eukaryotic DNA topoisomerase I introduces transient single-stranded breaks on double-stranded DNA and spontaneously breaks down single-stranded DNA. The cleavage sites on both single and double-stranded SV40 DNA have been determined by DNA sequencing. Consistent with other reports, the eukaryotic enzymes, in contrast to prokaryotic type I topoisomerases, links to the 3'-end of the cleaved DNA and generates a free 5'-hydroxyl end on the other half of the broken DNA strand. Both human and calf enzymes cleave SV40 DNA at identical and specific sites. From 827 nucleotides sequenced, 68 cleavage sites were mapped. The majority of the cleavage sites were present on both double and single-stranded DNA at exactly the sane nucleotide positions, suggesting that the DNA sequence is essential for enzyme recognition. By analyzing all the cleavage sequences, certain nucleotides are found to be less favored at the cleavage sites. There is a high probability to exclude G from positions -4, -2, -1 and +1, T from position -3, and A from position -1. These five positions(-4 to +1 oriented in the 5' to 3' direction) around the cleavage sites must interact intimately with topo I and thus are essential for enzyme recognition. One topo I cleavage site which shows an atypical cleavage sequence maps in the middle of a palindromic sequence near the origin of SV40 DNA replication. It occurs only on single-stranded SV40 DNA, suggesting that the DNA hairpin can alter the cleavage specificity. The strongest cleavage site maps near the origin of SV40 DNA replication at nucleotide 31-32 and has a pentanucleotide sequence of 5'-TGACT-3'.",
author = "Edwards, {Kenneth A.} and Halligan, {Brian D.} and Davis, {John L.} and Nivera, {Nadine L.} and Leroy-Fong Liu",
year = "1982",
month = "4",
day = "24",
doi = "10.1093/nar/10.8.2565",
language = "English",
volume = "10",
pages = "2565--2576",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "8",

}

TY - JOUR

T1 - Recognition sites of eukaryotic DNA topoisomerase I

T2 - DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA

AU - Edwards, Kenneth A.

AU - Halligan, Brian D.

AU - Davis, John L.

AU - Nivera, Nadine L.

AU - Liu, Leroy-Fong

PY - 1982/4/24

Y1 - 1982/4/24

N2 - Eukaryotic DNA topoisomerase I introduces transient single-stranded breaks on double-stranded DNA and spontaneously breaks down single-stranded DNA. The cleavage sites on both single and double-stranded SV40 DNA have been determined by DNA sequencing. Consistent with other reports, the eukaryotic enzymes, in contrast to prokaryotic type I topoisomerases, links to the 3'-end of the cleaved DNA and generates a free 5'-hydroxyl end on the other half of the broken DNA strand. Both human and calf enzymes cleave SV40 DNA at identical and specific sites. From 827 nucleotides sequenced, 68 cleavage sites were mapped. The majority of the cleavage sites were present on both double and single-stranded DNA at exactly the sane nucleotide positions, suggesting that the DNA sequence is essential for enzyme recognition. By analyzing all the cleavage sequences, certain nucleotides are found to be less favored at the cleavage sites. There is a high probability to exclude G from positions -4, -2, -1 and +1, T from position -3, and A from position -1. These five positions(-4 to +1 oriented in the 5' to 3' direction) around the cleavage sites must interact intimately with topo I and thus are essential for enzyme recognition. One topo I cleavage site which shows an atypical cleavage sequence maps in the middle of a palindromic sequence near the origin of SV40 DNA replication. It occurs only on single-stranded SV40 DNA, suggesting that the DNA hairpin can alter the cleavage specificity. The strongest cleavage site maps near the origin of SV40 DNA replication at nucleotide 31-32 and has a pentanucleotide sequence of 5'-TGACT-3'.

AB - Eukaryotic DNA topoisomerase I introduces transient single-stranded breaks on double-stranded DNA and spontaneously breaks down single-stranded DNA. The cleavage sites on both single and double-stranded SV40 DNA have been determined by DNA sequencing. Consistent with other reports, the eukaryotic enzymes, in contrast to prokaryotic type I topoisomerases, links to the 3'-end of the cleaved DNA and generates a free 5'-hydroxyl end on the other half of the broken DNA strand. Both human and calf enzymes cleave SV40 DNA at identical and specific sites. From 827 nucleotides sequenced, 68 cleavage sites were mapped. The majority of the cleavage sites were present on both double and single-stranded DNA at exactly the sane nucleotide positions, suggesting that the DNA sequence is essential for enzyme recognition. By analyzing all the cleavage sequences, certain nucleotides are found to be less favored at the cleavage sites. There is a high probability to exclude G from positions -4, -2, -1 and +1, T from position -3, and A from position -1. These five positions(-4 to +1 oriented in the 5' to 3' direction) around the cleavage sites must interact intimately with topo I and thus are essential for enzyme recognition. One topo I cleavage site which shows an atypical cleavage sequence maps in the middle of a palindromic sequence near the origin of SV40 DNA replication. It occurs only on single-stranded SV40 DNA, suggesting that the DNA hairpin can alter the cleavage specificity. The strongest cleavage site maps near the origin of SV40 DNA replication at nucleotide 31-32 and has a pentanucleotide sequence of 5'-TGACT-3'.

UR - http://www.scopus.com/inward/record.url?scp=0020489806&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0020489806&partnerID=8YFLogxK

U2 - 10.1093/nar/10.8.2565

DO - 10.1093/nar/10.8.2565

M3 - Article

C2 - 6281736

AN - SCOPUS:0020489806

VL - 10

SP - 2565

EP - 2576

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 8

ER -