Issue 14, 2021

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

Abstract

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.

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

Supplementary files

Article information

Article type
Paper
Submitted
05 Janv. 2021
Accepted
16 Febr. 2021
First published
23 Febr. 2021
This article is Open Access
Creative Commons BY-NC license

RSC Adv., 2021,11, 8411-8419

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

J. Kaminský, V. Andrushchenko and P. Bouř, RSC Adv., 2021, 11, 8411 DOI: 10.1039/D1RA00076D

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. You can use material from this article in other publications, without requesting further permission from the RSC, provided that the correct acknowledgement is given and it is not used for commercial purposes.

To request permission to reproduce material from this article in a commercial publication, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party commercial publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements