EXTENDED THEORY OF THE ELECTROPHORETIC MOBILITY-SHIFT ANALYSIS OF NONSPECIFIC PROTEIN-DNA COMPLEXES, FEATURING COOPERATIVITY

The simulated electrophoretic mobility-shift behavior of a model syste m, in which the nonspecific binding of a protein to a DNA fragment is cooperative, was compared with the experimental behavior of the DNA: h istone-like bacterial protein (HU) system, It was concluded that the b inding of HU to an 88 bp DNA fragment is, at least, not highly coopera tive. The theory of mobility-shift analysis was extended even further to encompass high affinity sequence-specific binding of protein to a D NA fragment followed by weak nonspecific binding, the latter governed by conditional probabilities. In addition to featuring a ladder of inc remental protein-DNA complexes, the computed mobility-shift patterns p laced emphasis upon stabilization of weak, nonspecific complexes in ge l cages.