title: Strong physical constraints on sequence-specific target location by proteins on DNA molecules.
abstract: Sequence-specific binding to DNA in the presence of competing non-sequence-specific ligands is a problem faced by proteins in all organisms. It is akin to the problem of parking a truck at a loading bay by the side of a road in the presence of cars parked at random along the road. Cars even partially covering the loading bay prevent correct parking of the truck. Similarly on DNA, non-specific ligands interfere with the binding and function of sequence-specific proteins. We derive a formula for the probability that the loading bay is free from parked cars. The probability depends on the size of the loading bay and allows an estimation of the size of the footprint on the DNA of the sequence-specific protein by assaying protein binding or function in the presence of increasing concentrations of non-specific ligand. Assaying for function gives an 'activity footprint'; the minimum length of DNA required for function rather than the more commonly measured physical footprint. Assaying the complex type I restriction enzyme, EcoKI, gives an activity footprint of approximately 66 bp for ATP hydrolysis and 300 bp for the DNA cleavage function which is intimately linked with translocation of DNA by EcoKI. Furthermore, considering the coverage of chromosomal DNA by proteins in vivo, our theory shows that the search for a specific DNA sequence is very difficult; most sites are obscured by parked cars. This effectively rules out any significant role in target location for mechanisms invoking one-dimensional, linear diffusion along DNA.
authors.affiliation: School of Chemistry, The King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JJ, UK.
authors.forename: Henrik
authors.initials: H
authors.lastname: Flyvbjerg
authors.forename: Steven A
authors.initials: SA
authors.lastname: Keatch
authors.forename: David T F
authors.initials: DT
authors.lastname: Dryden
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D018983:DNA Footprinting; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008954:Models, Biological; D011485:Protein Binding
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA; D004262:DNA Restriction Enzymes; C089629:endodeoxyribonuclease EcoKI