Molecular dynamics simulation of the effects of cytosine methylation on structure of oligonucleotides

Methylation of the cytosine bases in CpG dinucleotides of DNA is important in many cellular functions including gene regulation, chromosome inactivati on, as well as in cancer and other diseases. In this report we investigate the structural effects of methylation of cytosines in CpG sites. Hereditary diseases are frequently caused by mutations in CpG dinucleotides. Aqueous solution molecular dynamics simulations of four mutational hotspot containi ng DNA octamers were carried out with and without methylated cytosines. No major overall conformational changes were found due to the 5-methyl group o f the cytosine base. We also applied potential of mean force calculations t o determine the changes in the stacking free energy surface for the deoxyri bodinucleoside monophosphate 5-methyl-cytidylyl-3 ' ,5 ' -guanosine compare d to the unmethylated form. The 5-methyl group of the cytosine base was fou nd to enhance the base stacking ability. Characteristic features of the fre e energy surface due to the 5-methyl group were the more pronounced minimum and higher free energy states until the conformations are totally unstacke d. Certain local alterations were pronounced in the conformation in the oli gonucleotides with methylated CpG dinucleotides. The significance of protei n-DNA interactions as a mutation mechanism was discussed. (C) 2001 Elsevier Science B.V. All rights reserved.