title: A flexible approach to the calculation of resonance energy transfer efficiency between multiple donors and acceptors in complex geometries.
abstract: Resonance energy transfer provides a practical way to measure distances in the range of 10-100 A between sites in biological molecules. Although the relationship between the efficiency of energy transfer and the distance between sites is well described for a single pair of fluorophores, the situation is more difficult when more than two fluorophores are present. Using a Monte Carlo calculation scheme, we demonstrate how resonance energy transfer can be used to measure distances between fluorophores in complex geometries. We demonstrate the versatility of the approach by calculating the efficiency of energy transfer for individual fluorophores randomly distributed in two and three dimensions, for linked pairs of donors and acceptors and pentameric structures of five linked fluorophores. This approach can be used to relate the efficiency of energy transfer to the distances between fluorophores, R0, molecular concentrations, laser power, and donor/acceptor ratios in ensembles of molecules or when many fluorophores are attached to a single molecule such as in multimeric proteins.
authors.affiliation: School of Biomedical, Biomolecular and Chemical Sciences, Biomedical Imaging and Analysis Facility, The University of Western Australia, Crawley, Australia. ben@theochem.uwa.edu.au
authors.forename: Ben
authors.initials: B
authors.lastname: Corry
authors.forename: Dylan
authors.initials: D
authors.lastname: Jayatilaka
authors.forename: Paul
authors.initials: P
authors.lastname: Rigby
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D004307:Dose-Response Relationship, Radiation; D004579:Electron Transport; D036681:Fluorescence Recovery After Photobleaching / Q000379:methods*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D005456:Fluorescent Dyes / Q000032:analysis / Q000737:chemistry* / Q000528:radiation effects; D007834:Lasers; D018499:Linear Energy Transfer / Q000528:radiation effects; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods*; D008956:Models, Chemical; D011485:Protein Binding; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000528:radiation effects; D011829:Radiation Dosage
chemical_list: D005456:Fluorescent Dyes; D011506:Proteins