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 journalArticlepeer-review

44 Scopus citations


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
Issue number1
StatePublished - Jan 9 2014

ASJC Scopus subject areas

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


Dive into the research topics of 'Photophysical and dynamical properties of doubly linked Cy3-DNA constructs'. Together they form a unique fingerprint.

Cite this