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Nucleic Acids Research, 2000, Vol. 28, No. 16 3083-3091
© 2000 Oxford University Press

DNA bending induced by DNA (cytosine-5) methyltransferases

Tamás Raskó, Csaba Finta and Antal Kiss*

Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, PO Box 521, Szeged 6701, Hungary

DNA bending induced by six DNA (cytosine-5) methyltransferases was studied using circular permutation gel mobility shift assay. The following bend angles were obtained: M.BspRI (GGm5CC), 46–50°; M.HaeIII (GGm5CC), 40–43°; M.SinI (GGWm5CC), 34–37°; M.Sau96I (GGNm5CC), 52–57°; M.HpaII (Cm5CGG), 30°; and M.HhaI (Gm5CGC), 13°. M.HaeIII was also tested with fragments carrying a methylated binding site, and it was found to induce a 32° bend. A phase-sensitive gel mobility shift assay, using a set of DNA fragments with a sequence-directed bend and a single methyltransferase binding site, indicated that M.HaeIII and M.BspRI bend DNA toward the minor groove. The DNA curvature induced by M.HaeIII contrasts with the lack of DNA bend observed for a covalent M.HaeIII–DNA complex in an earlier X-ray study. Our results and data from other laboratories show a correlation between the bending properties and the recognition specificities of (cytosine-5) methyltransferases: enzymes recognizing a cytosine 3' to the target cytosine tend to induce greater bends than enzymes with guanine in this position. We suggest that the observed differences indicate different mechanisms employed by (cytosine-5) methyltransferases to stabilize the helix after the target base has flipped out.

* To whom correspondence should be addressed. Tel: +36 62 432 080; Fax: +36 62 433 506; Email: kissa@nucleus.szbk.u-szeged.huPresent address:Csaba Finta, Center for Nutrition and Toxicology, Department of Biosciences at NOVUM, Karolinska Institute, 141 57 Huddinge, Sweden


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