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Nucleic Acids Research Advance Access originally published online on October 16, 2007
Nucleic Acids Research 2007 35(19):6681-6689; doi:10.1093/nar/gkm721
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Nucleic Acids Research, 2007, Vol. 35, No. 19 6681-6689
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acid Enzymes

A hexanucleotide sequence (dC1–dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4

Hiroyuki Ohshima, Nobutaka Hirano and Hideo Takahashi*

Department of Applied Biological Science, Nihon University College of Bioresource Sciences, Fujisawa-shi, Kanagawa 252-8510, Japan

*To whom correspondence should be addressed. Tel: +81 466 84 3350; Fax: +81 466 84 3698; Email: htakaha{at}brs.nihon-u.ac.jp

Received June 7, 2007. Revised August 21, 2007. Accepted August 31, 2007.

Endonuclease (Endo) IV encoded by denB of bacteriophage T4 is an enzyme that cleaves single-stranded (ss) DNA in a dC-specific manner. Previously we have demonstrated that a dTdCdA is most preferable for Endo IV when an oligonucleotide substrate having a single dC residue is used. Here we demonstrate that Endo IV cleaves ssDNAs exclusively at the 5'-proximal dC where a sequence comprises dC residues both at the 5' proximal and 3' proximal positions (a dCs tract-dependent cleavage). The dCs tract-dependent cleavage is efficient and occurs when a dCs tract has at least 6 bases. Some dCs tracts larger than 6 bases behave as that of 6 bases (an extended dCs tract), while some others do not. One decameric dCs tract was shown to be cleavable in a dCs tract-dependent manner, but that with 13 dCs was not. The dCs tract-dependent cleavage is enhanced by the presence of a third dC residue at least for a 6 or 7 dCs tract. In contrast to the dCs tract-dependent cleavage, a dCs tract-independent one is generally inefficient and if two modes are possible for a substrate DNA, a dCs tract-dependent mode prevails. A model for the dCs tract-dependent cleavage is proposed.


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