Structural Study of Methylated and Non-Methylated Duplexes by IR Fourier Spectroscopy

Structure of the duplex consisting of 23 pairs of bases was studied before and after the methylation of two cytosine molecules from different chains of the duplex. The study was performed in a buffer solution using an IR Fourier spectrometer. The absorption bands corresponding to the duplex backbone were found to change their characteristics after the methylation. Firstly, the integrated intensity ratio of the absorption bands, S1044/S1085, decreased by a factor of 1.5. The absorption band at 1044 cm-1 corresponds to the COC bond of deoxyribose, and the band at 1085 cm-1 to the PO2symm.vibr bond. Secondly, a substantial shift of the absorption band 1085→1112 cm-1 (Δν = 27 cm-1) was observed. In addition, pronounced changes in the absorption region of CH stretching vibrations took place. In particular, shifting of some absorption bands assigned to the stretching vibrations of CH bonds; the 2979→2945.7 shift was equal to 33.3 cm-1. In addition to the indicated changes, some bands corresponding to the Z structure appeared in the methylated duplex. Thus, methylation of two cytosine molecules in the duplex leads to the order→order structural transition, most likely to the B→Z transition.