Gal repressosome assembly and repression of the gal operon in E. coli occurs when two dimeric GalR proteins and the histone-like HU protein bind to cognate sites causing DNA looping. Negatively supercoiled DNA is absolutely required for the repressosome formation, which prevents analysis of this 113 bp loop by conventional techniques. Structure-based genetic analysis defined the GalR surfaces interacting to form a stacked, V-shaped, tetrameric structure (similar to that of the LacI tetramer). In principle, this tetrameric structure is compatible with four different looping modes of DNA, two parallel and two antiparallel. Based on the sequence-dependent structural parameters of the interoperator DNA and conformation changes caused by GalR and HU binding, we constructed stereochemical models for the four possible DNA loops. The harmonic energy functions included in this model account for the sequence-specific anisotropic bending and twisting of the duplex at the level of dimeric steps (1). They also incorporate the strong cross-correlation between the DNA bending and twisting. Evaluation of the DNA elastic energies gave unambiguous preference to a novel loop structure in which the two gal operators adopt an antiparallel orientation causing undertwisting of DNA. The 92 bp lac loop can also adopt a similar trajectory. We suggest the antiparallel Gal-like DNA loops may serve as putative elementary units of the prokaryotic chromatin architecture.

1. Olson, W.K., Gorin, A.A., Lu, X., Hock, L. & Zhurkin, V.B. (1998) Proc. Natl. Acad. Sci. USA 95, 11163-11168.