Specific binding of cruciform DNA structures by a protein from human extracts.

A gel electrophoresis binding assay has been used to probe extracts from cultured human lymphoblasts for proteins that bind cruciform structures in duplex DNA. Proteins have been detected that form complexes with synthetic X- and Y-junctions. Several lines of evidence suggest that binding is specific for DNA structure rather than sequence: (1) X- and Y-structures were bound whereas linear duplexes containing identical DNA sequences were not, (2) Binding occurred with equal efficiency to two X-junctions that were constructed from DNA strands of different sequence, (3) One X-junction successfully competed with another for binding whereas linear duplex DNA did not; and (4) protein-DNA complexes were observed at probe:non-specific competitor DNA ratios of 1:10,000.     

New insight into the recognition of branched DNA structure by junction-resolving enzymes

Junction-resolving enzymes are nucleases that exhibit structural selectivity for the four-way (Holliday) junction in DNA. In general, these enzymes both recognize and distort the structure of the junction. New insight into the molecular recognition processes has been provided by two recent co-crystal structures of resolving enzymes bound to four-way DNA junctions in highly contrasting ways. T4 endonuclease VII binds the junction in an open conformation to an approximately flat binding surface whereas T7 endonuclease I envelops the junction, which retains a much more three-dimensional structure. Both proteins make contacts with the DNA backbone over an extensive area in order to generate structural specificity. The comparison highlights the versatility of Holliday junction resolution, and extracts some general principles of recognition.     

Endonuclease VII has two DNA-binding sites each composed from one N- and one C-terminus provided by different subunits of the protein dimer.

Endonuclease VII (endo VII) is a Holliday structure-resolving enzyme of bacteriophage T4. Its activity depends on dimerization, DNA binding and hydrolysis of two phosphodiester bonds flanking the Holliday junction. We analysed the DNA-binding activity of truncated monomeric and covalently linked dimeric endo VII proteins. We show that both ends of endo VII are involved in DNA binding. In particular, the C-terminus of one subunit interacts with the N-terminus of the other subunit, constituting one DNA-binding site; the other two termini form the second binding site of the dimer. One binding site is sufficient to bind cruciform DNA. The concerted mechanism involving termini from different subunits ensures that only dimers bind to Holliday structures, thus providing two catalytic centres which introduce two cleavages in opposite strands. This is a precondition for precise resolution of Holliday structures.     

Specific recognition of four-way DNA junctions by the C-terminal zinc-binding domain of HPV oncoprotein E6

E6 is an oncoprotein implicated in cervical cancers produced by " high risk " human papillomaviruses. E6 binds specifically to several cellular proteins, including the tumour suppressor p53 and the ubiquitin ligase E6-AP. However, E6 is also a DNA-binding protein which recognizes a structural motive present in four-way junctions. Here, we demonstrate that the C-terminal zinc-binding domain of E6, expressed separately from the rest of the protein, fully retains the selective four-way junction recognition activity. The domain can bind to two identical and independent sites on a single junction, whereas full-length E6 can only bind to one site. The junction bound to either one or two domains adopts an extended square conformation. These results allow us to assign the structure-dependent DNA recognition activity of E6 to its C-terminal domain, which therefore represents a new class of zinc-stabilized DNA-binding module. Comparison with the binding characteristics of other junction-specific proteins enlightens the rules which govern protein-induced deformation of four-way DNA junctions.     

Human placental endonuclease cleaves Holliday junctions

A partially purified endonuclease from human placenta cleaves cruciform structures. The placental enzyme is active both on extruded cruciform structures from negatively supercoiled covalently closed circular plasmid DNA and on synthetic X-junctions formed by reannealing short oligonucleotides. Plasmids containing natural or cloned palindromes such as pBR322 and pHD101-3 were used as substrates. The synthetic X-junction tetramer DNA formed by reannealing short oligonucleotides, was converted into dimer form by the enzyme. This is the first report of an enzyme activity involved in resolution of recombination intermediates in higher eukaryotes and second report of a cellular enzyme.