Protein-DNA binding in the absence of specific base-pair recognition.

Journal Article (Journal Article)

Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)-DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF-DNA binding preferences. We used high-throughput protein-DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying repeat symmetries. Based on statistical mechanics modeling, we identify a new protein-DNA binding mechanism induced by DNA sequence symmetry in the absence of specific base-pair recognition, and experimentally demonstrate that this mechanism indeed governs protein-DNA binding preferences.

Full Text

Duke Authors

Cited Authors

  • Afek, A; Schipper, JL; Horton, J; Gordân, R; Lukatsky, DB

Published Date

  • December 2, 2014

Published In

Volume / Issue

  • 111 / 48

Start / End Page

  • 17140 - 17145

PubMed ID

  • 25313048

Pubmed Central ID

  • PMC4260554

Electronic International Standard Serial Number (EISSN)

  • 1091-6490

Digital Object Identifier (DOI)

  • 10.1073/pnas.1410569111


  • eng

Conference Location

  • United States