Hithell, Gordon, González-Jiménez, Mario, Greetham, Gregory M et al. (6 more authors) (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 : PCCP. pp. 10333-10342. ISSN 1463-9084
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © the Owner Societies 2017 |
Keywords: | Base Pairing,DNA/chemistry,Nucleic Acid Conformation,Phase Transition,Solvents/chemistry,Spectrophotometry, Infrared,Transition Temperature |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Chemistry (York) |
Depositing User: | Pure (York) |
Date Deposited: | 01 Feb 2019 10:20 |
Last Modified: | 14 Jan 2025 00:11 |
Published Version: | https://doi.org/10.1039/c7cp00054e |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1039/c7cp00054e |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:141900 |