Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs

John W. Trauger, Eldon E. Baird, Milan Mrksich, Peter B. Dervan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

104 Scopus citations

Abstract

The sequence-specific recognition of the minor groove of DNA by pyrrole-imidazole polyamides has been extended to 9-13 base pairs (bp). Four polyamides, ImPyPy-Py-PyPyPy-Dp, ImPyPy-G-PyPyPy-Dp, ImPyPy-β-PyPyPy-Dp, and ImPyPy-γ-PyPyPy-Dp (Im = N-methylimidazole, Py = N-methylpyrrole, Dp = N,N-dimethylaminopropylamide, G = glycine, β = β-alanine, and γ = γ-aminobutyric acid), were synthesized and characterized with respect to their DNA-binding affinities and specificities at sequences of composition 5'-(A,T)G(A,T)5C(A,T)-3' (9 bp) and 5'-(A,T)5G(A,T)C(A,T)5-3' (13 bp). In both sequence contexts, the β-alanine-linked compound ImPyPy-β-PyPyPy-Dp has the highest binding affinity of the four polyamides, binding the 9 bp site 5'-TGTTAAACA-3' (K(a) = 8 x 108 M-1) and the 13 bp site 5'-AAAAAGACAAAAA-3' (K(a) = 5 x 109 M-1) with affinities higher than the formally N-methylpyrrole-linked polyamide ImPyPy-Py-PyPyPy-Dp by factors of ~8 and ~85, respectively (10 mM Tris·HCl, 10 mM KCl, 10 mM MgCl2, and 5 mM CaCl2, pH 7.0). The binding data for ImPyPy-γ-PyPyPy-Dp, which has been shown previously to bind DNA in a 'hairpin' conformation, indicates that γ-aminobutyric acid does not effectively link polyamide subunits in an extended conformation. These results expand the binding site size targetable with pyrrole-imidazole polyamides and provide structural elements that will facilitate the design of new polyamides targeted to other DNA sequences.

Original languageEnglish (US)
Pages (from-to)6160-6166
Number of pages7
JournalJournal of the American Chemical Society
Volume118
Issue number26
DOIs
StatePublished - Jul 3 1996

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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