Wrapping of flanking non-operator DNA in lac repressor-operator complexes:implications for DNA looping

In our studies of lac repressor tetramer (T)-lac operator (O) interactions, we observed that the presence of extended regions of non-operator DNA flan king a single lac operator sequence embedded in plasmid DNA produced large and unusual cooperative and anticooperative effects on binding constants (K -obs) and their salt concentration dependences for the formation of 1:1 (TO ) and especially 1:2 (TO2) complexes. To explore the origin of this strikin g behavior we report and analyze binding data on 1:1 (TO) and 1:2 (TO2) com plexes between repressor and a single O-sym operator embedded in 40 bp, 101 bp, and 2514 bp DNA, over very wide ranges of [salt]. We find large interr elated effects of flanking DNA length and [salt] on binding constants (K-ob s(TO), K-obs(TO2)) and on their [salt]-derivatives, and quantify these effe cts in terms of the free energy contributions of two wrapping modes, design ated local and global. Both local and global wrapping of flanking DNA occur to an increasing extent as [salt] decreases. Global wrapping of plasmid-le ngth DNA is extraordinarily dependent on [salt]. We propose that global wra pping is driven at low salt concentration by the polyelectrolyte effect, an d involves a very large number (greater than or similar to 20) of coulombic interactions between DNA phosphates and positively charged groups on lac r epressor. Coulombic interactions in the global wrap must involve both the c ore and the second DNA-binding domain of lac repressor, and result in a com plex which is looped by DNA wrapping. The non-coulombic contribution to the free energy of global wrapping is highly unfavorable (similar to + 30-50 k cal mol(-1)), which presumably results from a significant extent of DNA dis tortion and/or entropic constraints. We propose a structural model for glob al wrapping, and consider its implications for looping of intervening non-o perator DNA in forming a complex between a tetrameric repressor (LacI) and one multi-operator DNA molecule in vivo and in vitvo. The existence of DNA wrapping in LacI-DNA interactions motivates the proposal that most if not a ll DNA binding proteins may have evolved the capability to wrap and thereby organize flanking regions of DNA. (C) 1999 Academic Press.