Physical Sciences and Mathematics Commons^™

Single Molecule Studies Of A Short Rna, Peker Milas

Doctoral Dissertations

The material related with orientation of Cyanine dyes and their behavior at the ends of duplex RNA is also documented in [110]. Cyanine dyes are widely used to study the folding and structural transformations of nucleic acids using fluorescence resonance energy transfer (FRET). The extent to which FRET can be used to extract inter- and intra-molecular distances has been the subject of considerable debate in the literature; the contribution of dye and linker dynamics to the observed FRET signal is particularly troublesome. We used molecular dynamics (MD) simulations to study the dynamics of the indocarbocyanine dyes Cy3 and Cy5 attached …