MD Simulations and FRET Studies of Dye-Labeled RNA

Abstract

Fluorescence resonance energy transfer (FRET) is a powerful technique for understanding the structural transformations of RNA, DNA and proteins. With a few notable exceptions, the contribution of fluorophore and linker dynamics to these FRET measurements has not generally been investigated. Towards a better understanding of FRET on dye-labeled RNA, we present molecular dynamic (MD) simulations of 16mer double-stranded RNA with cyanine dyes attached at either the 3’ or 5’ ends with a 3 carbon linker. Water is included explicitly, and both dyes are in the ground state configuration. Differences in these two labeling strategies are discussed. We compare our simulations to data taken both on surface-attached and droplet-confined molecules. The effect of relative dye orientation and distance fluctuations due to the flexible linker are explicitly investigated.