Paper Citing NAMD - Abstract
Shu, Dan; Zhang, Hui; Petrenko, Roman; Meller, Jarek; Guo, Peixuan
Dual-Channel Single-Molecule Fluorescence Resonance Energy Transfer to Establish Distance Parameters for RNA Nanoparticles
ACS NANO, 4:6843-6853, NOV 2010
The increasing interest in RNA nanotechnology and the demonstrated feasibility of using RNA nanoparticles as therapeutics have prompted the need for imaging systems with nanometer-scale resolution for RNA studies Phi29 dimeric pRNAs can serve as building blocks in assembly into the hexameric ring of the nanomotors; as modules of RNA nanoparciles, and as vehides for specific delivery of the rapeutics to cancers or viral infected cells The understanding of the 3D structure of this novel RNA dimeric particle is fundamentally and practically important Although a 3D model of pRNA dimer has been proposed based on biochemical analysis, no distance measurements or X ray diffraction data have been reported here we evaluated the application of our customized single-molecule dual viewing system for distance measurement within pRNA dimers using single-molecule Fluorescence Resonance Energy Transffer (smFRET) Ten pRNA monomers labeled with single donor or acceptor fluorophores at various locations were constructed and eight dimers were assembled smFRET signals were detected for six simers The tethered arm sizes of the fluorophores were estimated empirically from dual labeled RNA/DNA standards The distances between donor and acceptor were calculated and used as distance parameters to assess and refine the previously reported 3D model of the dimers bound Distances between nucleotides in pRNA dimers were found to be different from those of the dimers bound to procapsid, suggesting a conformational change of hte pRNA dimer upon binding to the procapsid
