RNA structural forms studied by vibrational circular dichroism: Ab initio interpretation of the spectra

Infrared (IR) and vibrational circular dichroism (VCD) spectra of single-stranded poly(rA) and poly(rU) RNA polynucleotides and double- and triple-stranded RNA helices were recorded and interpreted on the basis of density functional theory (DFT) at the BPW91/6-31G** level. Ab initio computations were performed for smaller fragments and extended to longer oligomers via transfer of atomic property tensors. The normal mode partial optimization method developed lately was found convenient for relaxation of the fragment geometries. Most of observed spectral features could be assigned to vibrations of the adenine, uracil, and sugar-phosphate chromophores; in particular, the VCD band shapes could be explained on the basis of specific spatial interactions. Thus, the VCD technique proved to be sensitive to various RNA conformational types (random coil, single strand, duplex, and triplex) in solution, spectra of which could be reliably modeled. The effect of the solvent could be only partially included, and ambiguity remains in the model structure used for the triplex RNA form.