<br/>Vibrational spectroscopy, such as linear and 2D IR spectroscopy, provides a powerful tool to detect the secondary and tertiary structures of nucleic acids and their conformational dynamics due to the sensitivity of specific normal modes, in particular the base carbonyl stretch modes, to the hydrogen bonding patterns and the three-dimensional structures of these biomolecules. Combining molecular dynamics simulations and our recently developed vibrational frequency maps and coupling models, we have computed the linear and 2D IR spectra of a set of nucleobase derivatives and oligonucleotides and demonstrated that the predicted spectra are in quantitative agreement with experiments. We further reveal how the observed spectral features result from the local electrostatic environment of the chromophores and the inter-base interactions, and how they change with the geometric arrangements of the oligonucleotides. We thus provide a novel theoretical strategy to model the infrared spectra of oligonucleotides, which will help elucidate the experimental spectra at the molecular level.

Modeling the infrared spectroscopy of oligonucleotides

ACS Fall 2021

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