Enhanced sequence specific recognition in the minor groove of DNA by covalent peptide dimers: bis(pyridine-2-carboxamidonetropsin)(CH_2)_(3-6)

Abstract

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-carboxamidenetropsin)(CH_2)_(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.

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