The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level

Marathe, Arvind ; Bansal, Manju (2010) The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level Journal of Physical Chemistry B, 114 (16). pp. 5534-5546. ISSN 1520-6106

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Official URL: http://pubs.acs.org/doi/abs/10.1021/jp911055x

Related URL: http://dx.doi.org/10.1021/jp911055x

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.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:47424
Deposited On:11 Jul 2011 05:22
Last Modified:11 Jul 2011 05:22

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