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Nucleic Acids Res. 2014 Apr;42(6):3821-32. doi: 10.1093/nar/gkt1316. Epub 2013 Dec 25.

Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA.

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Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana, IL 61801, USA, Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801, USA, RIKEN, Cellular and Molecular Biology Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801, USA.


Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20-500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.

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