Nucleic Acids Research, 2002, Vol. 30, No. 10 2183-2192
© 2002 Oxford University Press
Thymine-methyl/
interaction implicated in the sequence-dependent deformability of DNA
Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan and 1The CHPI Institute, 3-10-7 Narusedai, Machida-shi, Tokyo 194-0043, Japan
The crystal structures of deoxy-oligonucleotides were retrieved from the Nucleic Acid Database and analyzed with the use of our program CHPI. The structure of 5'-ApTpApT-3' has been shown to be stabilized by the 5-methyl group in the thymidine moiety that favorably interacts with the adenine 
-ring preceding it. H2' of the deoxyribose in adenine also interacts with the thymine ring next to it. Since a 5'-ApT-3' sequence is accompanied by another 5'-ApT-3' in the complementary strand, the interaction is duplicated, thus forming a ‘twin A/T-Me interaction’. Coordinates of oligonucleotides with A-T rich sequences were retrieved and analyzed. In almost every case, the thymidine 5-methyl group favorably interacts with an adenine ring in the same strand. The structure of duplexes incorporating A-tracts was also analyzed. The 5-methyl group in the thymidine moiety has been found to interact favorably with the base -ring before it. Since an A-tract is lined with an oligo-T sequence in the complementary strand, a successive N/T-Me stacking may contribute in making the A-tracts robust and straight. The possible involvement of the N/T-Me and the twin A/T-Me motif in the deformability of DNA has been suggested. The role of methyl groups in modified DNA has been discussed on a similar basis.
* To whom correspondence should be addressed. Tel: +81 3 3441 4173; Fax: +81 3 3441 7589; Email: umezaway{at}bikaken.or.jpThis paper is dedicated to the late Professor Max F. Perutz, the founder of structural biology. The authors sincerely regret the immeasurable loss of an outstanding figure in the world of science