Premium
Theoretical studies on the mobility‐shift assay of protein‐DNA complexes
Author(s) -
Cann John R.
Publication year - 1998
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.1150190202
Subject(s) - electrophoretic mobility shift assay , dna , chemistry , electrophoresis , macromolecule , molecule , dna binding protein , biophysics , stoichiometry , binding site , chemical physics , gene , biochemistry , transcription factor , biology , organic chemistry
The theory of mass transport coupled to revesible macromolecular interactions under chemical kinetic control forms the basis for computer simulation of the electrophoretic mobility‐shift behavior of protein‐DNA complexes. Model systems include (i) specific binding of a univalent protein molecule to a single site on the DNA molecule; (ii) the putative cage effect; (iii) cooperative binding to multiple sites; (iv) formation of looped complexes of 1:1 and 2:1 stoichiometry; (v) noncooperative and cooperative, nonspecific binding modes; and (vi) binding of dimerizing transcriptional factors to response elements of target genes. Favorable comparison of simulated with experimental mobility‐shift behavior indicates that the phenomenological mechanisms, whereby observed mobility‐shift patterns are generated during electrophoresis, are embodies in the theory. These studies have provided guidelines for definitive interpretation of mobility‐shift assays and for the design of experiments to develop a detailed understanding of the particular system under investigation.