The general affinity of lac repressor for E. coli DNA: Implications for gene regulation in procaryotes and eucaryotes

Structural aspects of protein-DNA recognition

“…278 PROTEIN-DNA COMPLEXES Even proteins that recognize specific target sequences of DNA have significant affinity for non-cognate sequences (or bulk DNA); the non-specific binding to DNA is probably an essential property of all DNA-binding proteins. Indeed, von Hippel et al (1974) and Lin & Riggs (1975) have shown that, for simple bacterial repressors at least, the ratio of the affinity for specific binding to that of non-specific binding should be of the order 105 to allow control of expression in response to changes of allosteric effectors. DNA-protein interactions are in many instances highly dependent on the concentration of mono-and di-valent cations and pH.…”

A comparison of invivo and invitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos

“…We suggest that there are several key differences between these predictions and the widespread DNA binding of homeoproteins in Drosophila. First, in contrast to the poor discrimination between most genes shown by homeoproteins, prokaryotic regulators are predicted to bind to their target genes at levels at least 100-1000 times higher than they bind to any other region of the genome (Lin and Riggs, 1975;Biggin, 1998). Secondly, many prokaryotic transcription factors bind with high affinity to 14-20 bp specific sequences that occur rarely in the genome, whereas homeoproteins bind to degenerate 6 bp sequences that are found in most Drosophila genes at a density of 5-10 sites per kb of DNA (Walter and Biggin, 1996; D.Dalma-Weiszhausz and M.D.Biggin, unpublished data).…”

Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1.

“…It is important to note that all of the histone H 1C protein may not be incorporated into individual nucleosomal particles, rather like transcription factors may interact with DNA both specifically or nonspecifically (Lin and Riggs 1975). Although histone HI protein binds preferentially to DNA wrapped around the core histones rather than to naked DNA (Hayes and Wolffe 1993), under physiological ionic conditions histone H1 is readily exchanged between DNA that is either naked or wrapped around the core histones within a nucleosome (Thomas and Rees 1983;van Holde 1989).…”