Specific and non specific Escherichia coli ribonucleic acid polymerase DNA complexes are not hydrodynamically equivalent in analytical band sedimentation.
We have measured the sedimentation coefficients (s) of different DNA molecules of a few thousand base bairs in the presence of increasing amounts of E. coli RNA polymerase under conditions where tight binding complexes are formed. The measured s does not increase linearly with n(n=RNA Polymerase/DNA molar ratio); the s vs n plot can be decomposed into two parts; first the increase in s is small until n reaches a value n0 approximately equal to the number of strong promoters of the DNA molecule under consideration, then when n greater than n0 the slope of s(n) is much higher. The observations are in agreement with a model which postulates that strong specific polymerase binding leads to an increase in frictional coefficient of the RNA Polymerase-DNA complex, while non specific(or less specific)RNAP binding leads to a contraction of the RNA Polymerase-DNA complexes.
D001665:Binding Sites; D002498:Centrifugation; D004269:DNA, Bacterial / Q000302:isolation & purification*; D012321:DNA-Directed RNA Polymerases / Q000302:isolation & purification*; D004926:Escherichia coli / Q000032:analysis*; D008956:Models, Chemical; D008968:Molecular Conformation
D004269:DNA, Bacterial; D012321:DNA-Directed RNA Polymerases