Published online 6 May 2004
Nucleic Acids Research, 2004, Vol. 32, No. 8 2494-2507
Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe
Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA and 1 Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
*To whom correspondence should be addressed. Tel: +1 803 777 1514; Fax: +1 803 777 1456; Email: berg{at}mail.chem.sc.edu
Present address:
Mark M. Somoza, Lehrstuhl für Physik Weihenstephan, Technische Universität München, Vöttinger Straße 40, 85350 Freising, Germany
Received as resubmission March 11, 2004; Revised and Accepted April 12, 2004
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 
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 We suggest that at the chain end, where DNA on one side of the probe has been replaced by water, the charge- stabilizing dynamics have the same overall amplitude, but that much of the relaxation occurs before the start of the measurement time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.