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Nucleic Acids Research Advance Access originally published online on May 8, 2007
Nucleic Acids Research 2007 35(10):e75; doi:10.1093/nar/gkm040
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Nucleic Acids Research, 2007, Vol. 35, No. 10 e75
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

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

Hugh P. Morgan1, Peter Estibeiro2, Martin A. Wear1, Klaas E.A. Max3, Udo Heinemann3, Liza Cubeddu4, Maurice P. Gallagher1, Peter J. Sadler5 and Malcolm D. Walkinshaw1,*

1Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK, 2Nyrion Ltd, ETTC Biospace, Kings Buildings, Edinburgh EH9 3JF, UK, 3Max-Delbrück-Centrum für Molekulare Medizin 13125 Berlin, Germany, 4School of Molecular and Microbial Bioscience, University of Sydney, Sydney, NSW, 2006, Australia and 5School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, UK

*To whom correspondence should be addressed. Tel: +44 (0) 131 650 7056; Fax: +44 (0) 131 650 7055; Email: m.walkinshaw{at}ed.ac.uk

Received October 10, 2006. Revised December 18, 2007. Accepted January 9, 2007.

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.


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[Abstract] [Full Text] [PDF]


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