Extended theory of the electrophoretic mobility‐shift analysis of nonspecific protein‐DNA complexes, featuring cooperativity

Abstract

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.