Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA

Hithell, G., González-Jiménez, M., Greetham, G. M., Donaldson, P. M., Towrie, M., Parker, A. W., Burley, G. A., Wynne, K. and Hunt, N. T. (2017) Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA. Physical Chemistry Chemical Physics, (doi:10.1039/C7CP00054E) (Early Online Publication)

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Abstract

Changes in the structural and solvation dynamics of a 15mer AT DNA duplex upon melting of the double-helix are observed by a combination of ultrafast two-dimensional infrared (2D-IR) and optical Kerr-effect (OKE) spectroscopies. 2D-IR spectroscopy of the vibrational modes of the DNA bases reveal signature off-diagonal peaks arising from coupling and energy transfer across Watson–Crick paired bases that are unique to double-stranded DNA (ds-DNA). Spectral diffusion of specific base vibrational modes report on the structural dynamics of the duplex and the minor groove, which is predicted to contain a spine of hydration. Changes in these dynamics upon melting are assigned to increases in the degree of mobile solvent access to the bases in single-stranded DNA (ss-DNA) relative to the duplex. OKE spectra exhibit peaks that are assigned to specific long-range phonon modes of ds- and ss-DNA. Temperature-related changes in these features correlate well with those obtained from the 2D-IR spectra although the melting temperature of the ds-DNA phonon band is slightly higher than that for the Watson–Crick modes, suggesting that a degree of long-range duplex structure survives the loss of Watson–Crick hydrogen bonding. These results demonstrate that the melting of ds-DNA disrupts helix-specific structural dynamics encompassing length scales ranging from mode delocalisation in the Watson–Crick base pairs to long-range phonon modes that extend over multiple base pairs and which may play a role in molecular recognition of DNA.

Item Type:Articles
Status:Early Online Publication
Refereed:Yes
Glasgow Author(s) Enlighten ID:Burley, Dr Glenn and Wynne, Professor Klaas
Authors: Hithell, G., González-Jiménez, M., Greetham, G. M., Donaldson, P. M., Towrie, M., Parker, A. W., Burley, G. A., Wynne, K., and Hunt, N. T.
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:06 April 2017
Copyright Holders:Copyright © 2017 Royal Society of Chemistry
First Published:First published in Physical Chemistry Chemical Physics 2017
Publisher Policy:Reproduced under a Creative Commons License

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