title: The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level.
abstract: DNA sequences containing a stretch of several A:T basepairs without a 5'-TA-3' step are known as A-tracts and have been the subject of extensive investigation because of their unique structural features such as a narrow minor groove and their crucial role in several biological processes. One of the aspects under investigation has been the influence of the 5-methyl group of thymine on the properties of A-tracts. Detailed molecular dynamics simulation studies of the sequences d(CGCAAAUUUGCG) and d(CGCAAATTTGCG) indicate that the presence of the 5-methyl group in thymine increases the frequency of a narrow minor groove conformation, which could facilitate its specific recognition by proteins, and reduce its susceptibility to cleavage by DNase I. The bias toward a wider minor groove in the absence of the thymine 5-methyl group is a static structural feature. Our results also indicate that the presence of the thymine 5-methyl group is necessary for calibrating the backbone conformation and the basepair and dinucleotide step geometry of the core A-tract as well as the flanking CA/TG and the neighboring GC/GC steps, as observed in free and protein-bound DNA. As a consequence, it also fine-tunes the curvature of the longer DNA fragment in which the A-tract is embedded.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore-12, India.
authors.forename: Arvind
authors.initials: A
authors.lastname: Marathe
authors.forename: Manju
authors.initials: M
authors.lastname: Bansal
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009038:Motion; D012091:Repetitive Sequences, Nucleic Acid; D013941:Thymine / Q000737:chemistry*
chemical_list: D004247:DNA; D013941:Thymine