Extended theory of the electrophoretic mobility-shift analysis of nonspecific protein-DNA complexes, featuring cooperativity.
The simulated electrophoretic mobility-shift behavior of a model system, in which the nonspecific binding of a protein to a DNA fragment is cooperative, was compared with the experimental behavior of the DNA: histone-like bacterial protein (HU) system. It was concluded that the binding of HU to an 88 bp DNA fragment is, at least, not highly cooperative. The theory of mobility-shift analysis was extended even further to encompass high affinity sequence-specific binding of protein to a DNA fragment followed by weak nonspecific binding, the latter governed by conditional probabilities. In addition to featuring a ladder of incremental protein-DNA complexes, the computed mobility-shift patterns placed emphasis upon stabilization of weak, nonspecific complexes in gel cages.
Coombs
R O
RO
Department of Biochemistry, The University of Colorado Medical School, Denver, USA.
Cann
J R
JR
D001426:Bacterial Proteins / Q000032:analysis*; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000032:analysis*; D004586:Electrophoresis; D015233:Models, Statistical; D011485:Protein Binding; D017186:Titrimetry
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C040330:histone-like protein HU, bacteria