Free-sliding ligands: An alternative model of DNA–protein interactions

✍ Scribed by Charles P. Woodbury Jr.

• Publisher: Wiley (John Wiley & Sons)
• Year: 1981
• Tongue: English
• Weight: 842 KB
• Volume: 20
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.1981.360201015

✦ Synopsis

Abstract

We present an alternative to the common lattice model for nonspecific DNA–protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one‐dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding‐site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee‐von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single‐stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).