Photophysical and dynamical properties of doubly linked Cy3-DNA constructs

Elana M S Stennett, Ning Ma, Arjan Van Der Vaart, Marcia Levitus

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Photophysical measurements are reported for Cy3-DNA constructs in which both Cy3 nitrogen atoms are attached to the DNA backbone by short linkers. While this linking was thought to rigidify the orientation of the dye and hinder cis-isomerization, the relatively low fluorescence quantum yield and the presence of a short component in the time-resolved fluorescence decay of the dye indicated that cis-isomerization remained possible. Fluorescence correlation spectroscopy and transient absorption experiments showed that photoisomerization occurred with high efficiency. Molecular dynamics simulations of the trans dye system indicated the presence of stacked and unstacked states, and free energy simulations showed that the barriers for stacking/unstacking were low. In addition, simulations showed that the ground cis state was feasible without DNA distortions. Based on these observations, a model is put forward in which the doubly linked dye can photoisomerize in the unstacked state.

Original languageEnglish (US)
Pages (from-to)152-163
Number of pages12
JournalJournal of Physical Chemistry B
Volume118
Issue number1
DOIs
StatePublished - Jan 9 2014

Fingerprint

DNA
Coloring Agents
Dyes
deoxyribonucleic acid
dyes
Fluorescence
Isomerization
fluorescence
isomerization
Photoisomerization
simulation
Quantum yield
nitrogen atoms
Ground state
Free energy
Molecular dynamics
Nitrogen
free energy
Spectroscopy
molecular dynamics

ASJC Scopus subject areas

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

Cite this

Photophysical and dynamical properties of doubly linked Cy3-DNA constructs. / Stennett, Elana M S; Ma, Ning; Van Der Vaart, Arjan; Levitus, Marcia.

In: Journal of Physical Chemistry B, Vol. 118, No. 1, 09.01.2014, p. 152-163.

Research output: Contribution to journalArticle

Stennett, Elana M S ; Ma, Ning ; Van Der Vaart, Arjan ; Levitus, Marcia. / Photophysical and dynamical properties of doubly linked Cy3-DNA constructs. In: Journal of Physical Chemistry B. 2014 ; Vol. 118, No. 1. pp. 152-163.
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