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

Abstract:

: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.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Spiriti J,Binder JK,Levitus M,van der Vaart A

doi

10.1016/j.bpj.2011.01.014

subject

Has Abstract

pub_date

2011-02-16 00:00:00

pages

1049-57

issue

4

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(11)00060-9

journal_volume

100

pub_type

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