Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe

Mark M. Somoza, Daniele Andreatta, Catherine J. Murphy, Robert S. Coleman, Mark A. Berg

Research output: Contribution to journalArticle

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 ∼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 We suggest that at the chain end, where DNA on one side of the probe has been replaced by water, the charge-stabilizing dynamics have the same overall amplitude, but that much of the relaxation occurs before the start of the measurement time window.

Original languageEnglish (US)
Pages (from-to)2494-2507
Number of pages14
JournalNucleic acids research
Volume32
Issue number8
DOIs
StatePublished - 2004
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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