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
Language
- eng
Conference Location
- United States