DNA ring closure mediated by protein HU

Abstract

The histone-like protein HU serves as an accessory factor that can facilitate the interaction of certain proteins with their specific DNA binding sites. Examples occur in different systems for prokaryotic DNA replication, transcription, and gene regulation. The protein-DNA interactions that are stimulated by HU generally involve coiling or looping of the DNA, and the possibility has been considered that HU exerts its effect by contributing flexibility to different DNA binding sites, but there has been no direct demonstration of this. To explore the possibility that HU can mediate tight DNA curvatures, we studied its effect on the formation of DNA circles when DNA ligase cyclizes short linear DNA fragments. It is demonstrated that HU greatly increases the cyclization rates of all fragments that were examined having lengths greater than 98 base pairs. Fragments of 99, 108, 120, or 126 base pairs could not cyclize in the absence of HU, but cyclization went rapidly with HU, showing that HU can mediate very tight DNA curvatures.