Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids

González-Jiménez, M. , Ramakrishnan, G., Tukachev, N. , Senn, H. M. and Wynne, K. (2021) Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids. Physical Chemistry Chemical Physics, 23(23), pp. 13250-13260. (doi: 10.1039/D0CP05404F) (PMID:34095914) (PMCID:PMC8207511)

Abstract

Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands of DNA) and B-DNA characterized using femtosecond optical Kerr-effect spectroscopy. Contrary to expectation, we found that G-quadruplexes show several strongly underdamped delocalized phonon-like modes that have the potential to contribute to the biology of the DNA at the atomic level. In addition, G-quadruplexes present modes at a higher frequency than B-DNA demonstrating that changes in the stiffness of the molecule alter its gigahertz to terahertz vibrational profile.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Senn, Dr Hans and Tukachev, Mr Nikita and Ramakrishnan, Dr Gopakumar and Wynne, Professor Klaas and Gonzalez Jimenez, Dr Mario
• Authors: González-Jiménez, M., Ramakrishnan, G., Tukachev, N., Senn, H. M., and Wynne, K.
• College/School: College of Science and Engineering > School of Chemistry
• Journal Name: Physical Chemistry Chemical Physics
• Publisher: Royal Society of Chemistry
• ISSN: 1463-9076
• ISSN (Online): 1463-9084
• Published Online: 01 June 2021
• Copyright Holders: Copyright © 2021 The Royal Society of Chemistry
• First Published: First published in Physical Chemistry Chemical Physics 23(23): 13250-13260
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
166776		The structure and dynamics of water confined in nanoscale pools: the dynamic crossover	Klaas Wynne	Engineering and Physical Sciences Research Council (EPSRC)	EP/J009733/1	Chemistry
190647		Solvation dynamics and structure around proteins and peptides: collective network motions vs. weak interactions	Klaas Wynne	Engineering and Physical Sciences Research Council (EPSRC)	EP/K034995/1	Chemistry
171830		EPSRC: Institutional Sponsorship 2015 - University of Glasgow	Miles Padgett	Engineering and Physical Sciences Research Council (EPSRC)	EP/N508792/1	Computing Science
303917		Delocalised phonon-like modes in organic and bio-molecules	Klaas Wynne	Leverhulme Trust (LEVERHUL)	RPG-2018-350	Chemistry
304469		CONTROL	Klaas Wynne	European Commission (EC)	832703	Chemistry