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Open Access Highly Accessed Research article

Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein

Esther E Biswas-Fiss12, Jirayu Kukiratirat1 and Subhasis B Biswas1*

Author Affiliations

1 Department of Molecular Biology, School of Osteopathic Medicine & Graduate School of Biomedical Sciences, University of Medicine & Dentistry of New Jersey, Stratford, NJ 08084, USA

2 Department of Bioscience Technologies, Jefferson School of Health Professions, Thomas Jefferson University, Philadelphia, PA 19107, USA

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BMC Biochemistry 2012, 13:10  doi:10.1186/1471-2091-13-10

Published: 14 June 2012

Abstract

Background

Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase.

Results

We have cloned and purified SSB from Bacillus anthracis (SSBBA). In the absence of DNA, at concentrations ≤100 μg/ml, SSBBA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSBBA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)70 binding suggested that SSBBA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure.

Conclusions

Unlike other prokaryotic SSB proteins, SSBBA from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSBBA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSBBA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSBBA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.

Keywords:
Single-stranded DNA binding protein (SSB); DNA replication; Fluorescence anisotropy; ssDNA binding; Protein-DNA complex