Investigation of Fluorescent DYE-DNA Interactions using Multidimensional Adaptive Umbrella Sampling Simulations

Abstract

Fluorescence resonance energy transfer is often used as a “molecular ruler” to measure distances between fluorescent dyes attached to a biomolecule. This technique relies on the assumption that these dyes rotate freely around the linkers that attach them to the molecule. In the case of Cy3 attached to the 5' end of DNA, it is known from NMR studies that the dye stacks on top of the first base pair, but recent fluorescence anisotropy studies show that there is still some rotation about the linker on short time scales. To explore the dynamics of this system more fully, we performed atomistic molecular dynamics simulations using GAMUS, a recently developed multidimensional adaptive umbrella sampling method. Using the method, the free energy basins of the DNA/Cy3 system were characterized in terms of five dihedral angles along the linker between Cy3 and the DNA.