DNA bending induced by DNA (cytosine-5) methyltransferases.
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.BSP:RI (GG(m5)CC), 46-50 degrees; M.HAE:III (GG(m5)CC), 40-43 degrees; M.SIN:I (GGW(m5)CC), 34-37 degrees; M.SAU:96I (GGN(m5)CC), 52-57 degrees; M.HPA:II (C(m5)CGG), 30 degrees; and M.HHA:I (G(m5)CGC), 13 degrees. M. HAE:III was also tested with fragments carrying a methylated binding site, and it was found to induce a 32 degrees 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.HAE:III and M. BSP:RI bend DNA toward the minor groove. The DNA curvature induced by M.HAE:III contrasts with the lack of DNA bend observed for a covalent M.HAE:III-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.
Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, PO Box 521, Szeged 6701, Hungary.
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D044503:5-Methylcytosine; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation; D004269:DNA, Bacterial / Q000737:chemistry*; D004270:DNA, Circular / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D015183:Restriction Mapping
D004269:DNA, Bacterial; D004270:DNA, Circular; D009838:Oligodeoxyribonucleotides; D044503:5-Methylcytosine; D003596:Cytosine; D004248:DNA (Cytosine-5-)-Methyltransferases