DNA aggregation by an archaeal DNA binding protein Sac10b and its novel DNA nicking activity
The solution structure of an archaeal DNA binding protein SaclOb (DBNP-B) by cross-linking with formaldehyde and its interaction with DNA were studied. Results indicated that SaclOb existed as oligomeric structure in solution and the oligomerization was greatly stimulated by Mg 2+ ions and elevated temperatures. In light of our earlier observation that SaclOb interacts with DNA forming different types of complexes with DNA at different protein concentrations, its DNA-binding properties were also studied. Results demonstrated that the protein formed rapidly sedimentable co-aggregation complexes with both native and denatured DNA in a protein concentration-dependent manner. These protein DNA complexes were fluid-like crystalline material at a protein DNA ratio (3-6:1 w/w). Gel mobility shift assays carried out to study the interaction of the protein with plasmid DNA indicated possible DNA nicking by the protein. The DNA nicking activity of SaclOb was optimal in pH range of 7-8.5 and was dependent on Mg 2+ ions. It was maximal at protein to DNA ratio of (8:1, w/w) and very little activity was observed above and below this ratio. Nicking of DNA at this ratio indicated structure-specific DNA nicking by the protein. The protein might have important multi-functional role in the DNA metabolism in this organism.