Enhanced Sequence Specific Recognition in the Minor Groove of DNA by Covalent Peptide Dimers: Bis(pyridine-2-carboxamidonetropsin)(CH2)3–6

Milan Mrksich, Peter B. Dervan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

102 Scopus citations


The designed peptide pyridine-2-carboxamidonetropsin (2-PyN) binds to the minor groove of double-helical DNA at two very different sequences, 5′-TTTTT-3′ and 5′-TGTCA-3′, with comparable energetics but quite different structures. 2-PyN likely binds the 5′-TTTTT-3′ site as a 1:1 complex, whereas 2-PyN binds 5′-TGTCA-3′ sites as a 2:1 complex. In order to enhance the binding affinity of 2-PyN for the 5′-TGTCA-3′ site, covalently linked dimers of 2-PyN have been synthesized wherein the nitrogens of the central pyrroles are connected with propyl, butyl, pentyl, and hexyl linkers. DNase I footprint titration experiments reveal that these bis(pyridine-2-carbox-amidenetropsin) (CH2)3-6 peptides bind to a 5′-TGTCA-3′ site with binding affinities 10-fold greater than that of 2-PyN. By taking advantage of the different structures of peptides bound in the minor groove, the ratio of binding affinities of 2-PyN for 5′-TGTCA-3′ and 5′-TTTTT-3′ sites have been altered from 1:1 to 25:1.

Original languageEnglish (US)
Pages (from-to)9892-9899
Number of pages8
JournalJournal of the American Chemical Society
Issue number22
StatePublished - Nov 1 1993

ASJC Scopus subject areas

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


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