How DNA coiling enhances target localization by proteins.
Many genetic processes depend on proteins interacting with specific sequences on DNA. Despite the large excess of nonspecific DNA in the cell, proteins can locate their targets rapidly. After initial nonspecific binding, they are believed to find the target site by 1D diffusion ("sliding") interspersed by 3D dissociation/reassociation, a process usually referred to as facilitated diffusion. The 3D events combine short intrasegmental "hops" along the DNA contour, intersegmental "jumps" between nearby DNA segments, and longer volume "excursions." The impact of DNA conformation on the search pathway is, however, still unknown. Here, we show direct evidence that DNA coiling influences the specific association rate of EcoRV restriction enzymes. Using optical tweezers together with a fast buffer exchange system, we obtained association times of EcoRV on single DNA molecules as a function of DNA extension, separating intersegmental jumping from other search pathways. Depending on salt concentration, targeting rates almost double when the DNA conformation is changed from fully extended to a coiled configuration. Quantitative analysis by an extended facilitated diffusion model reveals that only a fraction of enzymes are ready to bind to DNA. Generalizing our results to the crowded environment of the cell we predict a major impact of intersegmental jumps on target localization speed on DNA.
van den Broek
B
B
Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
Lomholt
M A
MA
Kalisch
S-M J
SM
Metzler
R
R
Wuite
G J L
GJ
D001665:Binding Sites; D004278:DNA, Superhelical / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004058:Diffusion; D007700:Kinetics; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers; D011485:Protein Binding; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)
D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; C056127:DNA modification methylase EcoRV; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)