Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair

Justin Spiriti, Jennifer K. Binder, Marcia Levitus, Arjan Van Der Vaart

Research output: Contribution to journalArticlepeer-review

62 Scopus citations


We characterized the effect of the first basepair on the conformational dynamics of the fluorescent dye Cy3 attached to the 5′ end of double-stranded DNA using Gaussian-mixture adaptive umbrella sampling simulations. In the simulations, the sampling of all five dihedral angles along the linker was enhanced, so that both stacked and unstacked states were sampled. The affinity of Cy3 for a T · A basepair (with the dye attached to T) was found to be significantly less than for the other basepairs. This was verified experimentally by measuring the activation energies for cis-trans isomerization of the dye. The simulation and experimental results indicate the existence of partially unstacked conformations amenable to photoisomerization. The simulations also showed that stacking of Cy3 straightens the DNA while stabilizing the first basepair. Our findings indicate that fluorescence is modulated by Cy3-DNA interactions in a sequence-dependent manner.

Original languageEnglish (US)
Pages (from-to)1049-1057
Number of pages9
JournalBiophysical journal
Issue number4
StatePublished - Feb 16 2011

ASJC Scopus subject areas

  • Biophysics


Dive into the research topics of 'Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair'. Together they form a unique fingerprint.

Cite this