High affinity binding of proteins HMG1 and HMG2 to semicatenated DNA loops

Here we show that HMG1 and HMG2 bind with a much higher affinity, at least 4 orders of magnitude higher, to a new structure, Form X, which consists of a DNA loop closed at its base by a semicatenated DNA junction, forming a DNA hemicatenane. The binding constant of HMG1 to Form X is higher than 5 × 1012 M-1, and the half-life of the complex is longer than one hour in vitro.Of all DNA structures described so far with which HMG1 and HMG2 interact, we have found that Form X, a DNA loop with a semicatenated DNA junction at its base, is the structure with the highest affinity by more than 4 orders of magnitude. This suggests that, if similar structures exist in the cell nucleus, one of the functions of these proteins might be linked to the remarkable property of DNA hemicatenanes to associate two distant regions of the genome in a stable but reversible manner.Proteins HMG1 and HMG2, two of the most abundant non histone proteins, have been known for more than 25 years (for a review see [1]), and their function has been the subject of varied investigations, especially since it was found that they contain a domain of homology with many proteins implicated in the control of development or of differentiation. As examples of recent studies are their immunocytochemical localization [2], the deletion of the gene coding for HMG1 by homologous recombination in transgenic mice [3], the effect of HMG1 or of the HMG domain on the assembly of certain nucleoproteic complexes [4], the observation of the binding of HMG1 to Oct and Hox proteins [5,6], to nuclear hormone receptors [7], or to p53 [8], the influence of HMG1 on the circularization of short DNA fragments [9,10], on V(D)J rearrangement in vitro [11,12], or on transcription [13,14]. HMG1 has also been recently implicated as a mediator of endotoxin lethality [15]. An important way of studying the function and the mechanism of action of proteins HMG1/2 has obviously been the search for molecular partners, and, starting from the as