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Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach.

Morgan HP, Estibeiro P, Wear MA, Max KE, Heinemann U, Cubeddu L, Gallagher MP, Sadler PJ, Walkinshaw MD

Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK.

We have developed a novel DNA microarray-based approach for identification of the sequence-specificity of single-stranded nucleic-acid-binding proteins (SNABPs). For verification, we have shown that the major cold shock protein (CspB) from Bacillus subtilis binds with high affinity to pyrimidine-rich sequences, with a binding preference for the consensus sequence, 5'-GTCTTTG/T-3'. The sequence was modelled onto the known structure of CspB and a cytosine-binding pocket was identified, which explains the strong preference for a cytosine base at position 3. This microarray method offers a rapid high-throughput approach for determining the specificity and strength of ss DNA-protein interactions. Further screening of this newly emerging family of transcription factors will help provide an insight into their cellular function.

Published 12 June 2007 in Nucleic Acids Res, 35(10): e75.
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