Theoretical studies on the mobility‐shift behavior of binary protein‐DNA complexes
- 1 January 1993
- journal article
- research article
- Published by Wiley in Electrophoresis
- Vol. 14 (1), 669-679
- https://doi.org/10.1002/elps.11501401107
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.Keywords
This publication has 32 references indexed in Scilit:
- Stability of a Lac repressor mediated "looped complex"Biochemistry, 1991
- Analysis of the gel electrophoresis of looped protein-DNA complexes by computer simulationJournal of Molecular Biology, 1990
- Bacterial Chromosome StructurePublished by Springer Nature ,1990
- A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosomeCell, 1984
- Free energy coupling within macromoleculesJournal of Molecular Biology, 1983
- Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: kinetic measurements and conclusionsBiochemistry, 1981
- Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous latticeJournal of Molecular Biology, 1974
- Binding constants from zone transport of interacting moleculesBiochemistry, 1973
- Kinetics of Competitive Processes when Reactive Fragments are Produced in PairsJournal of the American Chemical Society, 1955
- Some remarks about free radicals and the photochemistry of solutionsTransactions of the Faraday Society, 1934