HU binds and folds single-stranded DNA.
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.
Kamashev
Dmitri
D
Laboratoire de Physiologie Bacterienne, CNRS UPR 9073, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Paris, France.
Balandina
Anna
A
Mazur
Alexey K
AK
Arimondo
Paola B
PB
Rouviere-Yaniv
Josette
J
D020137:Base Pair Mismatch; D001665:Binding Sites; D002021:Buffers; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012965:Sodium Chloride / Q000737:chemistry
D002021:Buffers; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C116822:hns protein, E coli; D012965:Sodium Chloride; D004247:DNA