Determining the specificity of protein–DNA interactions

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Abstract
Sequence-specific transcription factors (TFs) control gene expression. New methods allow for the rapid and accurate determination of TF binding specificity. Medium-throughput methods using microfluidic devices or surface plasmon resonance (SPR) can determine binding affinities directly. Microarray methods, such as protein-binding microarray (PBM) and cognate site identifier (CSI), can lead to very high-throughput measurements of TF specificity with binding sites of up to about ten base pairs. High-throughput versions of SELEX, with or without multiple rounds of selection, can provide accurate binding site specificities rapidly. Bacterial one-hybrid methods can also be made high-throughput and give accurate binding site models. Computational models can utilize the high-throughput data to make predictions beyond the data itself, provide information about the interaction and help in the design of factors with novel specificity.