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

Gordon Hithell, Mario González-Jiménez, Gregory M. Greetham, Paul M. Donaldson, Michael Towrie, Anthony W. Parker, Glenn A. Burley, Klaas Wynne, Neil Hunt

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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.
Original languageEnglish
Number of pages10
JournalPhysical Chemistry Chemical Physics
Publication statusAccepted/In press - 3 Apr 2017

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Keywords

  • solvation dynamics
  • DNA
  • deoxyribonucleic acid
  • structural dynamics
  • ultrafast two-dimensional infrared spectroscopy
  • 2D-IR
  • optical Kerr-effect spectroscopy
  • OKE

Cite this

Hithell, G., González-Jiménez, M., Greetham, G. M., Donaldson, P. M., Towrie, M., Parker, A. W., ... Hunt, N. (Accepted/In press). Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA. Physical Chemistry Chemical Physics.