title: Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA.
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.
authors.affiliation: Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, UK. neil.hunt@strath.ac.uk.
authors.forename: Gordon
authors.initials: G
authors.lastname: Hithell
authors.forename: Mario
authors.initials: M
authors.lastname: González-Jiménez
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Greetham
authors.forename: Paul M
authors.initials: PM
authors.lastname: Donaldson
authors.forename: Michael
authors.initials: M
authors.lastname: Towrie
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Parker
authors.forename: Glenn A
authors.initials: GA
authors.lastname: Burley
authors.forename: Klaas
authors.initials: K
authors.lastname: Wynne
authors.forename: Neil T
authors.initials: NT
authors.lastname: Hunt
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D044367:Phase Transition; D012997:Solvents / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D044366:Transition Temperature
chemical_list: D012997:Solvents; D004247:DNA