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Microarray-based methods for understanding protein-DNA interactions have been developed in the last 6 years due to the need to introduce high-throughput technologies in this field. Protein-DNA microarrays utilise chips upon which a large number of DNA sequences may be printed or synthesised. Any DNA-binding protein may then be interrogated by applying either purified sample or cellular/nuclear extracts, subject to availability of a suitable detection system. Protein is simply added to the microarray slide surface, which is then washed and subjected to at least one further incubation with a labelled molecule which binds specifically to the protein of interest. The signal obtained is proportional to the level of DNA-binding protein bound to each DNA feature, enabling relative affinities to be calculated. Key factors for reproducible and accurate quantification of protein binding are: microarray surface chemistry; length of oligonucleotides; position of the binding site sequence; quality of the protein and antibodies; and hybridisation conditions.

Original publication




Journal article


Adv Biochem Eng Biotechnol

Publication Date





87 - 110


Binding Sites, Biotechnology, DNA, DNA-Binding Proteins, Oligonucleotide Array Sequence Analysis, Protein Array Analysis, Protein Binding, Reproducibility of Results, Sensitivity and Specificity, Transcription Factors