Bulletin of the American Physical Society
APS March Meeting 2012
Volume 57, Number 1
Monday–Friday, February 27–March 2 2012; Boston, Massachusetts
Session X40: Focus Session: Single Molecule Biological Physics - Nucleic Acids
2:30 PM–5:30 PM,
Thursday, March 1, 2012
Sponsoring Units: DBIO DPOLY DCOMP
Chair: Lori Goldner and Jennifer Ross, University of Massachusetts
Abstract ID: BAPS.2012.MAR.X40.1
Abstract: X40.00001 : From force-fields to photons: MD simulations of dye-labeled nucleic acids and Monte Carlo modeling of FRET*
2:30 PM–3:06 PM
Preview Abstract Abstract
(Physics Department, University of Massachusetts, Amherst)
Fluorescence resonance energy transfer (FRET) is a powerful technique for understanding the structural fluctuations and transformations of RNA, DNA and proteins. Molecular dynamics (MD) simulations provide a window into the nature of these fluctuations on a different, faster, time scale. We use Monte Carlo methods to model and compare FRET data from dye-labeled RNA with what might be predicted from the MD simulation. With a few notable exceptions, the contribution of fluorophore and linker dynamics to these FRET measurements has not been investigated. We include the dynamics of the ground state dyes and linkers in our study of a 16mer double-stranded RNA. Water is included explicitly in the simulation. Cyanine dyes are attached at either the 3' or 5' ends with a 3 carbon linker, and differences in labeling schemes are discussed.\\[4pt] Work done in collaboration with Peker Milas, Benjamin D. Gamari, and Louis Parrot.
*This work was supported by NSF grant MCB-0920139.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2012.MAR.X40.1
The American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics.
1 Physics Ellipse, College Park, MD 20740-3844
Editorial Office 1 Research Road, Ridge, NY 11961-2701 (631) 591-4000
Office of Public Affairs 529 14th St NW, Suite 1050, Washington, D.C. 20045-2001 (202) 662-8700