In Silico Footprinting of Ligands Binding to the Minor Groove of DNA

Nahoum Guillaume Hsuan Anthony, Guillaume Huchet, Blair Johnston, John Parkinson, Colin Suckling, Roger Waigh, Simon MacKay

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)


The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by 'in silico footprinting'. Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting.
Original languageEnglish
Pages (from-to)1896-1907
Number of pages11
JournalJournal of Chemical Information and Modeling
Issue number6
Publication statusPublished - 5 Oct 2005


  • Silico Footprinting
  • Ligands Binding
  • Minor Groove
  • DNA
  • energy minimization
  • noncovalent binding modes
  • X-ray crystallography


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