The role of CH/pi interactions implicated in the sequence-dependent deformability of DNA

The crystal structure of AT-rich deoxynucleotides was retrieved from the Nucleic Acid Database and analyzed with the use of our program CHPI. It has been found that the thymidine 5-methyl group favorably interacts with an adenine ring in the same strand. Since an AT sequence is accompanied with another AT in the complementary strand, the interaction is duplicated, thus forming a twin CH/pi interaction. An AT step becomes stickier than other sequences by the above network. A number of CH/pi contacts have also been found in the crystal structure of A-tract. A successive N/T-methyl stacking in the same strand may contribute in making these steps robust and straight. The role of methyl groups in modified DNA has been discussed on a similar basis.