Role of monovalent counterions in the ultrafast dynamics of DNA

Sobhan Sen, Latha A. Gearheart, Evan Rivers, Hai Liu, Robert S. Coleman, Catherine J. Murphy, Mark A. Berg

Research output: Contribution to journalArticlepeer-review


This paper examines the contribution of counterion motion to the electric-field dynamics in the interior of DNA. The electric field is measured by a coumarin fluorophore that is synthetically incorporated into an oligonucleotide, where it replaces a native base pair. The DNA is a 17-base-pair oligomer with no A- or G-tracts. Time-resolved Stokes-shift measurements on the coumarin are made from 40 ps to 40 ns with each of the alkali ions and or one of several tetraalkylammonium ions as the DNA counterion. With the possible exception of rubidium, there are no indications of site-specific binding of the counterions. For sodium and other ions with a smaller hydrodynamic radius, the dynamics are identical and are fit to a power law. For larger ions, there is a progressive increase in the rate of shifting after 1 ns. This effect correlates with the hydrodynamic radius of the counterion. The lack of change in the spectral shape of the emission shows that neither the broadly distributed power-law relaxation nor the extra nanosecond dynamics are due to heterogeneity in the relaxation rates of different helices.

Original languageEnglish (US)
Pages (from-to)13248-13255
Number of pages8
JournalJournal of Physical Chemistry B
Issue number26
StatePublished - Jul 6 2006
Externally publishedYes

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry


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