Probe position-dependent counterion dynamics in DNA: Comparison of time-resolved stokes shift of groove-bound to base-stacked probes in the presence of different monovalent counterions

Sachin Dev Verma, Nibedita Pal, Moirangthem Kiran Singh, Sobhan Sen

Research output: Contribution to journalArticlepeer-review

Abstract

Time-resolved fluorescence Stokes shifts (TRFSS) of 4′,6-diamidino-2- phenylindole (DAPI) inside the minor groove of DNA are measured in the presence of three different monovalent counterions: sodium (Na +), rubidium (Rb +), and tetrabutylammonium (TBA +). Fluorescence up-conversion and time-correlated single photon counting are combined to obtain the time-resolved emission spectra (TRES) of DAPI in DNA from 100 fs to 10 ns. Time-resolved Stokes shift data suggest that groove-bound DAPI can not sense the counterion dynamics because the ions are displaced by DAPI far from the probe-site. However, when these results are compared to the earlier base-stacked coumarin data, the same ions are found to affect the nanosecond dynamics significantly. This suggests that the ions come close to the probe-site, such that they can affect the dynamics when measured by base-stacked coumarin. These results support previous molecular dynamics (MD) simulation data of groove-bound and base-stacked probes inside DNA.

Original languageEnglish (US)
Pages (from-to)2621-2626
Number of pages6
JournalJournal of Physical Chemistry Letters
Volume3
Issue number18
DOIs
StatePublished - Sep 20 2012
Externally publishedYes

Keywords

  • Biophysical Chemistry and Biomolecules

ASJC Scopus subject areas

  • Materials Science(all)
  • Physical and Theoretical Chemistry

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