Papers In Press, published online ahead of print June 12, 2008
J. Biol. Chem, 10.1074/jbc.M800174200
Submitted on January 8, 2008
Accepted on June 12, 2008
Motion of a DNA sliding clamp observed by single molecule fluorescence spectroscopy
Ted A. Laurence, Youngeun Kwon, Aaron Johnson, Christopher W. Hollars, Mike O'Donnell, Julio A. Camarero, and Daniel Barsky
Chemistry, Materials, Earth, and Life Sciences, Lawrence Livermore National Laboratory, Livermore, CA 94550
Corresponding Author: laurence2{at}llnl.gov
DNA sliding clamps attach to polymerases and slide along DNA to allow rapid, processive replication of DNA. These clamps contain many positively charged residues which could curtail the sliding due to attractive interactions with the negatively charged DNA. By single-molecule spectroscopy we have observed a fluorescently-labeled sliding clamp (pol III
subunit or
clamp), loaded onto freely diffusing, single-stranded M13 circular DNA annealed with fluorescently labeled DNA oligomers of up to 90 bases. We find that the diffusion constant for the ß clamp diffusing along DNA is on the order of 1014 m2/s, at least three orders of magnitude less than that for diffusion through water alone. We also find evidence that the
clamp remains at the 3' end in the presence of E. coli single-stranded binding protein (SSB). These results may imply that the clamp not only acts to hold the polymerase on the DNA, but also prevents excessive drifting along the DNA.