| Comments |
P.1014 2nd paragraph: "Analysis of nonspecific binding equilibria: McGhee & von Hippel (ref 153) have derived a modified version of the Scatchard binding isotherm that has proved to be widely applicable in the analysis
of both electrostatic and intercalative types of binding to nucleic acid lattices [see e.g. (refs 141, 148)]. In a relatively simple and powerful way their probabilistic derivation incorporates the consequences of nearest-neighbor cooperativity and overlap. The latter effect is characterized by n, the number of contiguous sites (nucleotides) rendered inaccessible to further binding by the binding of one ligand. A potential ambiguity in the analysis of ligand-nucleic acid binding equilibria arises in the physical interpretation of n : does it represent a number of nucleotides or half that number of nucleotide pairs? For example, the value of n deduced for the nonspecific binding of lac repressor is approximately 24 nucleotides or (equivalently) 12 base pairs. The latter alternative suggests that the ligand occupies (sterically blocks) all radial access to the helix for ~1.2 helical turns. The former number indicates that over a span of ~2.4 helical turns only half of the cylindrical surface is inaccessible to further binding: this interpretation appears to be favored by evidence from electron microscopy on the nonspecific
DNA-repressor complexes (ref 154). Thus, a second repressor molecule could bind nonspecifically to the helical region opposite to a bound ligand. Electron microscopy (ref 155) and chemical modification experiments (ref 156) both indicate that the specific binding of lac repressor and RNA polymerase involves contacts on only one side of the DNA helix." |