Thymine-methyl/pi interaction implicated in the sequence-dependent deformability of DNA.
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 pi-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 pi-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.
Umezawa
Yoji
Y
Institute of Microbial Chemistry, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan. umezaway@bikaken.or.jp
Nishio
Motohiro
M
D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D019175:DNA Methylation; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D013936:Thymidine / Q000737:chemistry*
D009841:Oligonucleotides; D004247:DNA; D013936:Thymidine