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Nucleic Acids Research Advance Access originally published online on December 20, 2007
Nucleic Acids Research 2008 36(3):1026-1036; doi:10.1093/nar/gkm667
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Nucleic Acids Research, 2008, Vol. 36, No. 3 1026-1036
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acid Enzymes

HU binds and folds single-stranded DNA

Dmitri Kamashev1, Anna Balandina1, Alexey K. Mazur2, Paola B. Arimondo3 and Josette Rouviere-Yaniv1,*

1Laboratoire de Physiologie Bacterienne, CNRS UPR 9073, 2Laboratoire de Biochimie Théorique, CNRS UPR 9080 Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie and 3CNRS UMR5153; INSERM U565; MNHN USM0503; 43 rue Cuvier 75005 Paris, France

*To whom correspondence should be addressed. Tel: +33 1 58 41 51 41; Fax: +33 1 58 41 50 20; Email: yaniv{at}ibpc.fr

Received June 1, 2007. Revised July 19, 2007. Accepted August 13, 2007.

The nucleoid-associated protein HU plays an important role in bacterial nucleoid organization and is involved in numerous processes including transposition, recombination and DNA repair. We show here that HU binds specifically DNA containing mismatched region longer than 3 bp as well as DNA bulges. HU binds single-stranded DNA (ssDNA) in a binding mode that is reminiscent but different from earlier reported specific HU interactions with double-helical DNA lesions. An HU dimer requires 24 nt of ssDNA for initial binding, and 12 nt of ssDNA for each additional dimer binding. In the presence of equimolar amounts of HU dimer and DNA, the ssDNA molecule forms an U-loop (hairpin-like) around the protein, providing contacts with both sides of the HU body. This mode differs from the binding of the single-strand-binding protein (SSB) to ssDNA: in sharp contrast to SSB, HU binds ssDNA non-cooperatively and does not destabilize double-helical DNA. Furthermore HU has a strong preference for poly(dG), while binding to poly(dA) is the weakest. HU binding to ssDNA is probably important for its capacity to cover and protect bacterial DNA both intact and carrying lesions.

Present address: Dmitri Kamashev, Enhelgardt Institut of Molecular Biology RAS, 32, Valilov Str., Moscow, Russia.


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