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

Hithell, Gordon and González-Jiménez, Mario and Greetham, Gregory M. and Donaldson, Paul M. and Towrie, Michael and Parker, Anthony W. and Burley, Glenn A. and Wynne, Klaas and Hunt, Neil (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, 2017 (16). pp. 10333-10342. ISSN 1463-9084 (https://doi.org/10.1039/C7CP00054E)

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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.

ORCID iDs

Hithell, Gordon ORCID logoORCID: https://orcid.org/0000-0001-9107-3229, González-Jiménez, Mario, Greetham, Gregory M., Donaldson, Paul M., Towrie, Michael, Parker, Anthony W., Burley, Glenn A., Wynne, Klaas and Hunt, Neil ORCID logoORCID: https://orcid.org/0000-0001-7400-5152;
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