Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments

@article{citeulike:1833567, abstract = {Abstract: We describe a simple approach and present a straightforward numerical algorithm to compute the best fit shot-noise limited proximity ratio histogram (PRH) in single-molecule fluorescence resonant energy transfer diffusion experiments. The key ingredient is the use of the experimental burst size distribution, as obtained after burst search through the photon data streams. We show how the use of an alternated laser excitation scheme and a correspondingly optimized burst search algorithm eliminates several potential artifacts affecting the calculation of the best fit shot-noise limited PRH. This algorithm is tested extensively on simulations and simple experimental systems. We find that dsDNA data exhibit a wider PRH than expected from shot noise only and hypothetically account for it by assuming a small Gaussian distribution of distances with an average standard deviation of 1.6 \r{A}. Finally, we briefly mention the results of a future publication and illustrate them with a simple two-state model system (DNA hairpin), for which the kinetic transition rates between the open and closed conformations are extracted.}, address = {Department of Chemistry and Biochemistry, Department of Physiology, and California NanoScience Institute, University of California at Los Angeles, Los Angeles, California 90095, Physical Biosciences Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, and Department of Mathematics, Oregon State University, Corvallis, Oregon 97331}, author = {Nir, E. and Michalet, X. and Hamadani, K. M. and Laurence, T. A. and Neuhauser, D. and Kovchegov, Y. and Weiss, S. }, citeulike-article-id = {1833567}, doi = {10.1021/jp063483n}, journal = {J. Phys. Chem. B}, keywords = {alex, analysis, simulation, single\_molecule}, month = {November}, number = {44}, pages = {22103--22124}, posted-at = {2008-03-30 20:16:12}, priority = {0}, title = {Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments}, url = {http://dx.doi.org/10.1021/jp063483n}, volume = {110}, year = {2006} }

TY - JOUR ID - citeulike:1833567 L3 - citeulike-article-id:1833567 TI - Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments JF - J. Phys. Chem. B VL - 110 IS - 44 SP - 22103 EP - 22124 AD - Department of Chemistry and Biochemistry, Department of Physiology, and California NanoScience Institute, University of California at Los Angeles, Los Angeles, California 90095, Physical Biosciences Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, and Department of Mathematics, Oregon State University, Corvallis, Oregon 97331 N2 - Abstract: We describe a simple approach and present a straightforward numerical algorithm to compute the best fit shot-noise limited proximity ratio histogram (PRH) in single-molecule fluorescence resonant energy transfer diffusion experiments. The key ingredient is the use of the experimental burst size distribution, as obtained after burst search through the photon data streams. We show how the use of an alternated laser excitation scheme and a correspondingly optimized burst search algorithm eliminates several potential artifacts affecting the calculation of the best fit shot-noise limited PRH. This algorithm is tested extensively on simulations and simple experimental systems. We find that dsDNA data exhibit a wider PRH than expected from shot noise only and hypothetically account for it by assuming a small Gaussian distribution of distances with an average standard deviation of 1.6 Å. Finally, we briefly mention the results of a future publication and illustrate them with a simple two-state model system (DNA hairpin), for which the kinetic transition rates between the open and closed conformations are extracted. KW - alex KW - analysis KW - simulation KW - single_molecule AU - Nir, E AU - Michalet, X AU - Hamadani, KM AU - Laurence, TA AU - Neuhauser, D AU - Kovchegov, Y AU - Weiss, S PY - 2006/11/09/ UR - http://dx.doi.org/10.1021/jp063483n ER -