title: BII stability and base step flexibility of N6-adenine methylated GATC motifs.
abstract: The effect of N6-adenine methylation on the flexibility and shape of palindromic GATC sequences has been investigated by molecular dynamics simulations. Variations in DNA backbone geometry were observed, which were dependent on the degree of methylation and the identity of the bases. While the effect was small, more frequent BI to BII conversions were observed in the GA step of hemimethylated DNA. The increased BII population of the hemimethylated system positively correlated with increased stacking interactions between methylated adenine and guanine, while stacking interactions decreased at the TC step for the fully methylated strand. The flexibility of the AT and TC steps was marginally affected by methylation, in a fashion that was correlated with stacking interactions. The facilitated BI to BII conversion in hemimethylated strands might be of importance for SeqA selectivity and binding.
authors.affiliation: Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, FL 33620, USA.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Karolak
authors.affiliation: Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, FL 33620, USA. Electronic address: avandervaart@usf.edu.
authors.forename: Arjan
authors.initials: A
authors.lastname: van der Vaart
mesh_terms: D000225:Adenine / Q000737:chemistry* / Q000378:metabolism*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D019175:DNA Methylation; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs
chemical_list: D004247:DNA; D000225:Adenine
keywords: Adenine methylation; DNA conformation; Free energy; GATC sequence; Molecular dynamics