Long-range vibrational dynamics are directed by Watson-Crick base-pairing in duplex DNA

Hithell, Gordon and Shaw, Daniel J. and Donaldson, Paul M. and Greetham, Gregory M. and Towrie, Michael and Burley, Glenn A. and Parker, Anthony W. and Hunt, Neil T. (2016) Long-range vibrational dynamics are directed by Watson-Crick base-pairing in duplex DNA. Journal of Physical Chemistry B. ISSN 1520-6106 (https://doi.org/10.1021/acs.jpcb.6b02112)

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Abstract

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation leads to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. Based on observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramo-lecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single and double-stranded DNA.

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