title: Theoretical studies on the mobility-shift behavior of binary protein-DNA complexes.
abstract: The theory of mass transport coupled to reversible interactions under chemical kinetic control forms the basis for computer simulation of the electrophoretic mobility-shift behavior of binary protein-DNA complexes. Several systems have been modeled in terms of either (i) specific binding of a protein molecule to a single site on the DNA molecule; (ii) cooperative binding to two or three sites; (iii) noncooperative binding to two sites, both of which bind protein with equal affinity; (iv) statistical binding to multiple sites having identical intrinsic binding constants; or (v) protein-induced DNA loop formation. Both models (iii) and (v) embody the concept of reversible isomerization of protein-DNA complexes. The resulting simulations have provided fundamental information concerning (i) the factors governing the electrophoretic persistence and separation of protein-DNA complexes; (ii) the shape of experimental mobility-shift patterns; (iii) the generation of the protein-DNA ladder upon titration, for example, of the 203-base pair operator with lac repressor; and (iv) the theoretical bases for quantitative interpretation of the patterns in terms of thermodynamic and kinetic parameters. The practical implications of these findings are discussed.
authors.affiliation: Department of Biochemistry/Biophysics/Genetic, University of Colorado Health Sciences Center, Denver 80262.
authors.forename: J R
authors.initials: JR
authors.lastname: Cann
mesh_terms: D017920:Antiporters / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D004586:Electrophoresis; D004926:Escherichia coli / Q000235:genetics; D009690:Nucleic Acid Conformation; D009876:Operon; D012097:Repressor Proteins / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D017920:Antiporters; D004268:DNA-Binding Proteins; D012097:Repressor Proteins; C034811:tetracycline resistance-encoding transposon repressor protein; D004247:DNA