Design and Synthesis of DH-21: an Imidazole/Pyrrole Containing Hairpin Targeting ATGA Sequences within the DNA Minor Groove

Dorothy Harris
Furman University

DH-21 was designed and synthesized to preferentially bind to the sequence 5'-ATGA-3'within the DNA minor groove. It is a polyamide hairpin compound containing imidazole/pyrrole units, designed on the basis of the DNA recognition properties of netropsin and distamycin. Although other molecules such as DB-293, a non-polyamide, aromatic dication that is presently undergoing clinical evaluation for the treatment of trypanosomiasis, have been shown to bind preferentially to sequences containing the ATGA motif, DH-21 is the first polyamide hairpin designed to recognize such a sequence. The techniques of nuclear magnetic resonance spectroscopy, infrared spectroscopy, as well as time-of-flight mass spectroscopy were used to characterize the structure of DH-21. Competitive dialysis experiments were conducted using ten different DNA duplexes containing core sequences A3T3, AGCA, ATGA, CACG, ATGT, CCGG, CGCG, GGCC, TCGA, and TGCA. Equilibrium constants from these experiments showed DH-21 to bind preferentially to ATGA containing sequences when compared with the other sequences. The TM value for DH-21 and the DNA sequence ATGA was 5-6 C, indicating a relatively good interaction between DH-21 and the ATGA sequence. Ongoing DNase I footprinting and surface plasma resonance (SPR) analysis will validate the competitive dialysis data and determine whether DH-21 is binding to DNA in a 1:1 stoichiometric ratio as expected