Dimensionality of energy transfer between intercalated and surface-bound donor-acceptor pairs in DNA

摘要

The energy transfer among several fluorophores when bound to linear DNA has been studied. The intercalation and groove binding of the fluorophores and relatively large persistent length of DNA makes it a good model for one dimensional energy transfer. In this case, as predicted by Foerster's theory, the donor intensity decayed with a t$+1/6$/ time dependence. The presence of a finite volume with a restricted geometry leads to significantly different donor intensity decays from that predicted by Foerster's model. We used intercalated/groove-bound fluorophores as donors and transition metal ion complexes which only bind on the outside surface of the DNA as acceptors, to characterize energy transfer in a cylindrical geometry. Two models were used: a hard cylinder with a donor on the z-axis and acceptors on the surface, and a soft-boundary cylinder where a distribution of acceptors within a cylindrical volume was allowed. The energy transfer among intercalated/groove-bound donors and surface-bound acceptors in DNA can be described with soft-boundary cylindrical geometry with reasonable parameters.