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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 prefer- ence for the consensus sequence, 50-GTCTTTG/T-30. 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.

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