Supercoiling-dependent site-specific binding of HU to naked mu DNA

Using HU chemical nucleases to probe HU-DNA interactions, we report here fo r the first time site-specific binding of HU to naked DNA. An unique featur e of this interaction is the absolute requirement for negative DNA supercoi ling for detectable levels of site-specific DNA binding. The HU binding sit e is the Mu spacer between the L1 and L2 transposase binding sites. Our res ults suggest recognition of an altered DNA structure which is induced by DN A supercoiling. We propose that recruitment of HU to this naked DNA site in duces the DNA bending required for productive synapsis and transpososome as sembly. Implications of HU as a supercoiling sensor with a potential in viv o regulatory role are discussed. Finally, using HU nucleases we have also s hown that non-specific DNA binding by HU is stimulated by increasing levels of supercoiling. (C) 1999 Academic Press.