Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment

0541262 - ÚOCHB 2022 RIV GB eng J - Journal Article
Kaminský, Jakub - Andrushchenko, Valery - Bouř, Petr
Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment.
RSC Advances. Roč. 11, č. 14 (2021), s. 8411-8419. E-ISSN 2046-2069
R&D Projects: GA ČR(CZ) GA20-10144S; GA MŠMT LTAUSA18085; GA MŠMT(CZ) EF16_019/0000729
Research Infrastructure: e-INFRA CZ - 90140
Institutional support: RVO:61388963
Keywords : nucleosides * magnetic circular dichroism * density functional theory * spectra modelling
OECD category: Physical chemistry
Impact factor: 4.036, year: 2021
Method of publishing: Open access
https://doi.org/10.1039/D1RA00076D

Chiroptical spectroscopic methods are excellent tools to study structure and interactions of biomolecules. However, their sensitivity to different structural aspects varies. To understand the dependence of absorption, electronic and magnetic circular dichroism (ECD, MCD) intensities on the structure, dynamics and environment, we measured and simulated spectra of nucleosides and other nucleic acid model components. The conformation space was explored by molecular dynamics (MD), the electronic spectra were generated using time dependent density functional theory (TDDFT). The sum over state (SOS) method was employed for MCD. The results show that accounting for the dynamics is crucial for reproduction of the experiment. While unpolarized absorption spectroscopy is relatively indifferent, ECD reflects the conformation and geometry dispersion more. MCD spectra provide variable response dependent on the wavelength and structural change. In general, MCD samples the structure more locally than ECD. Simple computational tests suggest that the optical spectroscopies coupled with the computational tools provide useful information about nucleic acid components, including base pairing and stacking.
Permanent Link: http://hdl.handle.net/11104/0318852