Energy Transfer in Single-Stranded DNA-Templated Stacks of Naphthalene Chromophores

Abstract

We have investigated energy transfer in a novel self-assembled DNA hybrid structure composed of diaminopurine-equipped naphthalene derivatives that are hydrogen-bonded along a single-stranded oligothymine template. By performing time-resolved measurements of the naphthalene donor luminescence decay in the absence and presence of a cyanine Cy3.5 acceptor bonded covalently to the 5′ end of the oligothymine, we have examined the role of temperature and DNA template length on energy transfer from donors to the acceptor. We find that energy transfer rates decline with increasing temperature over a fairly narrow (±5 °C) range over which changes in circular dichroism and donor luminescence lifetime indicate that the chiral assemblies are dissociating. In addition, the transfer rates exhibit a complex dependence on template length, increasing from initially low values for 10 bases toward an optimum for 30 bases and then declining again toward 60 bases. We find that for short (∼10 bases) templates, incomplete fill...