Raman Optical Activity as a Tool to Monitor Polynucleotide Conformation in Solutions.

Abstract

The reactivity and function of biopolymers depend on their structure and flexibility. There is a limited number of methods that can be used for their studies in solutions. Among them, Raman optical activity (ROA) provides excellent sensitivity to conformational changes. So far, ROA studies of nucleic acid systems are relatively rare because of the complexity of these molecules and difficulties in interpretation of the spectra. To explore the link between spectral shapes and the structure, and to advance the experimental and computational methodologies, we measured Raman and ROA spectra of four oligonucleotides (polyA, polyC, polyG, and polyU) in a wide wavenumber range. Molecular dynamics (MD) and density functional theory (DFT) were used for the spectra simulations. Temperature-dependent vibrational spectral changes are consistent with melting curves obtained from electronic circular dichroism (ECD). The results show that the spectra well-reflect molecular geometry, including changes caused by temperature variation. Comparison of theoretical and experimental Raman and ROA intensities appears as a convenient way to validate and potentially develop MD force fields; the RNA.Shaw force field provided results superior to the RNA.OL3 one. The combined spectroscopic and computational methodology thus can be used as a powerful means to study solution properties of nucleic acids.