Polar destabilization of DNA duplexes with single-stranded overhangs by the Deinococcus radiodurans SSB protein.
The Deinococcus radiodurans SSB protein has an occluded site size of 50 +/- 2 nucleotides on ssDNA but can form a stable complex with a 26-30-nucleotide oligodeoxynucleotide using a subset of its four ssDNA binding domains. Quantitative estimates of D. radiodurans SSB protein in the D. radiodurans cell indicate approximately 2500-3000 dimers/cell, independent of the level of irradiation. At biologically relevant concentrations, when bound at single-strand-double-strand DNA junctions in vitro, D. radiodurans SSB protein has a limited capacity to displace the shorter strand of the duplex, permitting it to bind to single-strand extensions shorter than 26-30 nucleotides. The capacity to displace the shorter strand of the duplex shows a pronounced bias for extensions with a free 3' end. The Escherichia coli SSB protein has a similar but somewhat less robust capacity to displace a DNA strand annealed adjacent to a single-strand extension. These activities are likely to be relevant to the action of bacterial SSB proteins in double-strand break repair, acting at the frayed ends created by ionizing radiation.
Eggington
Julie M
JM
Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, USA.
Kozlov
Alexander G
AG
Cox
Michael M
MM
Lohman
Timothy M
TM
D004247:DNA / Q000096:biosynthesis* / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D034301:Deinococcus / Q000235:genetics* / Q000378:metabolism*; D019281:Dimerization; D009691:Nucleic Acid Denaturation; D011485:Protein Binding; D013379:Substrate Specificity
D004268:DNA-Binding Proteins; D004247:DNA