title: Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe.
abstract: This paper explores the effects of structural modifications on the fast dynamics of DNA and the ability of time-resolved Stokes shift spectroscopy to measure those changes. The time-resolved Stokes shift of a synthetic coumarin base-pair replacement within an oligomer is measured between 40 ps and 40 ns. Comparisons are made between 17mers without modification, with a deleted base near the coumarin and with the coumarin placed near the end of the oligomer. The deletion of a next-to-nearest-neighbor base pair does not change the subnanosecond dynamics, but does cause an additional motion with a time constant of approximately 20 ns. A candidate for this motion is the flipping of the abasic sugar out of the helix and the concomitant intrusion of water into the interior of the helix. A nearby chain end causes little change in the dynamics after 1 ns but leads to a reduction in the amplitude of the dynamics between 40 ps and 1 ns. We suggest that at the chain end, where DNA on one side of the probe has been replaced by water, the charge- stabilizing dynamics have the same overall amplitude, but that much of the relaxation occurs before the start of the measurement time window.
authors.affiliation: Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Somoza
authors.forename: Daniele
authors.initials: D
authors.lastname: Andreatta
authors.forename: Catherine J
authors.initials: CJ
authors.lastname: Murphy
authors.forename: Robert S
authors.initials: RS
authors.lastname: Coleman
authors.forename: Mark A
authors.initials: MA
authors.lastname: Berg
mesh_terms: D020029:Base Pairing; D002942:Circular Dichroism; D003374:Coumarins / Q000378:metabolism*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004249:DNA Damage; D007700:Kinetics; D018583:Pliability; D013050:Spectrometry, Fluorescence; D013997:Time Factors
chemical_list: D003374:Coumarins; D004247:DNA; C030123:coumarin