Enhanced Sequence Specific Recognition in the Minor Groove of DNA by Covalent Peptide Dimers: Bis(pyridine-2-carboxamidonetropsin)(CH₂)_3–6

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.