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PMID: 8948651 Published · ppublish English Journal Article

Cleavage of single- and double-stranded DNAs containing an abasic residue by Escherichia coli exonuclease III (AP endonuclease VI).

Nucleic acids research ·Vol. 24 ·No. 22 ·1996-11-15 ·Pages 4572-6

Shida T, Noda M, Sekiguchi J

Abstract

The Escherichia coli exonuclease III (AP endonuclease VI) is a DNA-repair enzyme that hydrolyzes the phosphodiester bond 5' to an abasic site in DNA. To study how the enzyme recognizes the abasic site, we used oligonucleotides containing a synthetic abasic site at any desired position in the sequence. We prepared oligonucleotides containing an abasic residue such as 2'-deoxyribosylformamide, 2'-deoxyribose, 1',2'-dideoxy ribofuranose or propanediol. Duplex oligonucleotides containing an abasic residue used in this study were cleaved on the 5' side of the abasic site by exonuclease III in spite of the varieties of the bases opposite and adjacent to the abasic site. In addition, we observed that the enzyme cleaved single-stranded oligonucleotides containing an abasic site on the 5' side of the abasic site. These findings suggest that the enzyme may principally recognize the DNA-pocket formed at an abasic site. The indole ring of the tryptophan 212 residue of the exonuclease III is probably intercalated to the abasic site. The tryptophan in the vicinity of the catalytic site is conserved in the type II AP endonuclease from various organisms.

MeSH Terms
DNA, Bacterial/metabolism DNA, Single-Stranded/metabolism Escherichia coli/enzymology Exodeoxyribonucleases/metabolism Structure-Activity Relationship Substrate Specificity
Chemicals
DNA, Bacterial DNA, Single-Stranded Exodeoxyribonucleases exodeoxyribonuclease III
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Shida T
Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Nagano, Japan. shida@pterus.shinshu-u.ac.jp
Noda M
Sekiguchi J
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/24.22.4572
Email
shida@pterus.shinshu-u.ac.jp
Published
1996-11-15
Pages
4572-6
Language
English
Region
England
NLM ID
0411011
PMCID
PMC146277
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/24.22.4572 PMC Full Text View journal details
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