Individual nucleotide bases, not base pairs, are critical for triggering site-specific DNA cleavage by vaccinia topoisomerase.

The Journal of Biological Chemistry
Ligeng TianS Shuman

Abstract

Vaccinia DNA topoisomerase forms a covalent DNA-(3'-phosphotyrosyl)-enzyme intermediate at a specific target site 5'-C(+5)C(+4)C(+3)T(+2)T(+1)p downward arrow N(-1) in duplex DNA. Here we study the effects of abasic lesions at individual positions of the scissile and nonscissile strands on the rate of single-turnover DNA transesterification and the cleavage-religation equilibrium. The rate of DNA incision was reduced by factors of 350, 250, 60, and 10 when abasic sites replaced the -1N, +1T, +2T, and +4C bases of the scissile strand, but abasic lesions at +5C and +3C had little or no effect. Abasic lesions in the nonscissile strand in lieu of +4G, +3G, +2A, and +1A reduced the rate of cleavage by factors of 130, 150, 10, and 5, whereas abasic lesions at +5G and -1N had no effect. The striking positional asymmetry of abasic interference on the scissile and nonscissile strands highlights the importance of individual bases, not base pairs, in promoting DNA cleavage. The rate of single-turnover DNA religation by the covalent topoisomerase-DNA complex was insensitive to abasic sites within the CCCTT sequence of the scissile strand, but an abasic lesion at the 5'-OH nucleoside (-1N) of the attacking DNA strand slowed the rate of reli...Continue Reading

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Citations

Dec 25, 2008·Nucleic Acids Research·Nicole M BakerAlfonso Mondragón
Feb 20, 2008·Archives of Microbiology·B J HensonS R Barnum
Jul 21, 2010·Bioorganicheskaia khimiia·D V Bugreev, G A Nevinskiĭ
Dec 22, 2005·The Journal of Biological Chemistry·Asmita PatelAlfonso Mondragón
Sep 29, 2006·The Journal of Biological Chemistry·Lyudmila YakovlevaStewart Shuman
Nov 24, 2011·Nature Reviews. Molecular Cell Biology·Seychelle M VosJames M Berger

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