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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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PhysBinder: Improving the prediction of transcription factor binding sites by flexible inclusion of biophysical

Stefan Broos1, Arne Soete, Bart Hooghe

  • 1Department for Molecular Biomedical Research, VIB, Ghent University, B-9052 Ghent, Belgium.

Nucleic Acids Research
|April 27, 2013
PubMed

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
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