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Theoretical studies on the mobility‐shift behavior of binary protein‐DNA complexes
Author(s) -
Cann John R.
Publication year - 1993
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.11501401107
Subject(s) - chemistry , dna , lac repressor , electrophoretic mobility shift assay , molecule , operator (biology) , titration , base pair , repressor , chemical physics , biophysics , biochemistry , biology , lac operon , gene expression , organic chemistry , transcription factor , plasmid , gene
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.