Abstract
We have previously found that the presence of an H-type excitonic dimer formed by two fluorophores covalently bound to an oligonucleotide allows the delivery of such a polymer into live cells without inducing toxicity. We are now using time-resolved fluorescence measurements in solution to understand the molecular dynamics of an antisense probe and how pairing with complementary sense strands of various lengths and degrees of complementarity affects the antisense strand's properties. We report that a DNA strand composed of 30 residues and labeled with an H-type excitonic Cyanine-5/Cyanine-5 dimer shows a predominant 1.9 ns lifetime decay term accompanied by a shorter (0.5 ns) secondary lifetime. Similar values were measured for this excitonic dimer-bearing antisense strand following binding with a series of sense strands of varying lengths and compositions. However, significant differences in both time-resolved and steady-state anisotropy values were found, depending on the level of duplex formation through hydrogen bonding between sense and antisense sequences. More specifically, the anisotropy measurements of the double-labeled single-chain probe showed increases as the two intramolecular fluorophores were induced to separate with values dependent on the length and sequence of complementary sense strands. These differences suggest induced changes in the degrees of wobbling, tumbling, and spinning.
Published Version
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