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

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Item Type:Article
Title:Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach
Creators Name:Morgan, H.P. and Estibeiro, P. and Wear, M.A. and Max, K.E. and Heinemann, U. and Cubeddu, L. and Gallagher, M.P. and Sadler, P.J. and Walkinshaw, M.D.
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.
Keywords:Archaeal Proteins, Bacterial Proteins, Base Sequence, Binding Sites, Competitive Binding, Calorimetry, Carbocyanines, Consensus Sequence, Cytosine, Single-Stranded DNA, DNA-Binding Proteins, Electrophoretic Mobility Shift Assay, Fluorescent Dyes, Heat-Shock Proteins, Molecular Models, Oligonucleotide Array Sequence Analysis
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:e75
Date:May 2007
Official Publication:https://doi.org/10.1093/nar/gkm040
PubMed:View item in PubMed

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