Determining DNA Binding Selectivity and Affinity of the Tetra-amide Phenyl Imidazole Pyrrole Imidazole

Faculty Mentor(s)

Dr. Moses Lee, Hope College
Dr. Balaji Babu, Hope College
Dr. Sameer Chavda, Hope College

Document Type


Publication Date



The authors thank NSF for support.


DNA minor groove sequence binding polyamides consist of Imidazole (Im) and Pyrrole (P) recognition units. The polyamide f-IPI [f (formyl), Im (imidazole) and Py (pyrrole)] is known to have the greatest binding affinity and selectivity among all formyl-triamides. Targeting the DNA sequence 5’ –ACGCGT-3’, the polyamide has a binding affinity of 108 M-1. While studies have shown P-IPI shows better binding selectivity for one turn of the minor groove (10 base pairs), this tetraamide is not synthetically favorable. This paper reports the binding selectivity and affinity testing of the tetraamide Ph-IPI, a tetraamide with a phenyl group acting as a substitute for pyrrole in the tetraamide P-IPI. Ph-IPI’s binding affinity to its cognate sequence 5’ –ACGCGT-3’ was compared to the related formyl-triamides and tetraamides binding to four non-cognate sequences. We have studied the biophysical/characteristics of Ph-IPI utilizing thermal denaturation (TM), circular dichroism (CD) and isothermal titration microcalorimetry (ITC). In addition further biological/biophysical characterization in progress include the use of DNA footprinting and surface plasmon resonance (SPR) performed by research collaborators to determine the tetraamide’s DNA binding selectivity and affinity.

This document is currently not available here.