Theoretical studies on the mobility-shift assay of protein-DNA complexes

Electrophoresis
J R Cann

Abstract

The theory of mass transport coupled to reversible 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 embodied 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.

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Citations

Dec 23, 2008·Biochimica Et Biophysica Acta·Wei-Feng XueJannette Carey
Feb 27, 2015·Applied Microbiology and Biotechnology·Cláudia M VicenteJesús F Aparicio
Sep 20, 2006·The Journal of Biological Chemistry·Zoya M PetrushenkoValentin V Rybenkov
May 25, 2021·Molecular Microbiology·Xuejiao SongJohn E Cronan

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