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 di fferent structures. 2-PyN likely binds the 5'-TTTTT-3' site as a 1:1 c omplex, whereas 2-PyN binds 5'-TGTCA-3' sites as a 2:1 complex. In ord er 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 ni trogens of the central pyrroles are connected with propyl, butyl, pent yl, and hexyl linkers. DNase I footprint titration experiments reveal that these bis(pyridine-2-carboxamidenetropsin)(CH2)3-6 peptides bind to a 5'-TGTCA-3' site with binding affinities 10-fold greater than tha t of 2-PyN. By taking advantage of the different structures of peptide s 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.