Modeling Fluorescently Tagged DNA and RNA Oligonucleotides for Direct Comparison to FRET Experiments

Faculty Mentor(s)

Dr. Brent Krueger, Hope College

Document Type


Publication Date



This research was supported by the Howard Hughes Medical Institute, the ACS-Petroleum Research Fund, the National Science Foundation MRI, REU, & CIEG programs, the Midwest Undergraduate Computation Chemistry Consortium, and Teragrid Cyberinfastructure.


We are developing a method for studying the structural dynamics of biomolecules which couples fluorescence spectroscopy and computational modeling, providing a more complete understanding than is possible with either technique alone. Before beginning MD simulations, force field parameters were developed for the fluorescent probes to be used in experimental studies. This was carried out by first using quantum mechanical calculations to determine low-energy conformers of the probe molecules and calculate electrostatic potentials for these conformers. The RESP charge fitting procedure was then used to derive atomic charges; all other parameters were assigned by analogy to pre-existing force field parameters. Several DNA- and RNA-fluorescent probe systems were explicitly solvated in water and equilibrated before beginning production molecular dynamics simulations. These MD simulations will be used to generate simulated fluorescence data for direct comparison to experimental bulk and single-molecule FRET data.

This document is currently not available here.