Modifying the N-terminus of polyamides: PyImPyIm has improved sequence specificity over f-ImPyIm

Toni Brown, Hilary Mackay, Mark Turlington, Arden Sutterfield, Traci Smith, Alan Sielaff, Laura Westrate, Chrystal Bruce, Jerome Kluza, Caroline O'Hare, Binh Nguyen, W. David Wilson, John A. Hartley, Moses Lee

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f-ImPyIm, 1) were synthesized and the biochemical and biophysical chemistry evaluated. These compounds were synthesized with the aim of attaining a higher level of sequence selectivity over f-ImPyIm (1), a previously published strong minor-groove binder. Two compounds possessing a furan or a benzofuran moiety at the N-terminus showed a footprint of 0.5 μM at the cognate ACGCGT site (determined by DNase I footprinting); however, the specificity of these compounds was not improved. In contrast, PyImPyIm (4) produced a footprint of 0.5 μM but showed a superior specificity using the same technique. When evaluated by thermal melting experiments and circular dichroism using ACGCGT and the non-cognate AAATTT sequence, all compounds were shown to bind in the minor-groove of DNA and stabilize the cognate sequence much better than the non-cognate (except for the non-amido-compound that did not bind either sequence, as expected). PyImPyIm (4) was interesting as the ΔTm for this compound was only 4 °C but the footprint was very selective. No binding was observed for this compound with a third DNA (non-cognate, ACCGGT). ITC studies on compound 4 showed exothermic binding with ACGCGT and no heat change was observed for titrating the compound to the other two DNA sequences. The heat capacity (ΔCp) of the PIPI/ACGCGT complex calculated from the hydrophobic interactions and SASA calculations was comparable to the experimental value obtained from ITC (-146 cal mol-1 K-1). SPR results provided confirmation of the sequence specificity of PyImPyIm (4), with a Keq value determined to be 7.1 × 106 M-1 for the cognate sequence and no observable binding to AAATTT and ACCGGT. Molecular dynamic simulations affirmed that PyImPyIm (4) binds as a dimer in an overlapped conformation, and it fits snugly in the minor-groove of the ACGCGT oligonucleotide. PyImPyIm (4) is an especially interesting molecule, because although the binding affinity is slightly reduced, the specificity with respect to f-ImPyIm (1) is significantly improved.

Original languageEnglish (US)
Pages (from-to)5266-5276
Number of pages11
JournalBioorganic and Medicinal Chemistry
Issue number9
StatePublished - May 1 2008
Externally publishedYes


  • Binding
  • DNA
  • Minor-groove
  • N-terminus
  • Polyamide

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry


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