title: Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach.
abstract: 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.
authors.affiliation: Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK.
authors.forename: Hugh P
authors.initials: HP
authors.lastname: Morgan
authors.forename: Peter
authors.initials: P
authors.lastname: Estibeiro
authors.forename: Martin A
authors.initials: MA
authors.lastname: Wear
authors.forename: Klaas E A
authors.initials: KE
authors.lastname: Max
authors.forename: Udo
authors.initials: U
authors.lastname: Heinemann
authors.forename: Liza
authors.initials: L
authors.lastname: Cubeddu
authors.forename: Maurice P
authors.initials: MP
authors.lastname: Gallagher
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Sadler
authors.forename: Malcolm D
authors.initials: MD
authors.lastname: Walkinshaw
mesh_terms: D019843:Archaeal Proteins / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D002151:Calorimetry; D002232:Carbocyanines; D016384:Consensus Sequence; D003596:Cytosine / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D005456:Fluorescent Dyes; D006360:Heat-Shock Proteins / Q000378:metabolism; D008958:Models, Molecular; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D002232:Carbocyanines; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D005456:Fluorescent Dyes; D006360:Heat-Shock Proteins; C407094:cold shock protein, Bacillus; C085321:cyanine dye 5; D003596:Cytosine