DNA structural investigation through nitrile modification and IR spectroscopy

CHED 385

Michael E. Pitzer, mpitzer@fandm.edu and Edward E. Fenlon, efenlon@fandm.edu. Chemistry, Franklin and Marshall College, 501 Harrisburg Pike, Lancaster, PA 17604
This research involved modification and structural study of nucleosides and DNA oligomers by measuring the infrared (IR) absorption of a novel probe – a nitrile group. Indirectly, this method also provides a measure of the electronic environment of the nucleic acid species through the vibrational Stark effect (VSE). The syntheses of the CN–substituted nucleoside targets, including derivatives containing isotopic carbon and nitrogen in the nitrile group, were accomplished and their characteristic IR absorptions identified. Several nitrile–modified DNA oligomers have been prepared and studied. For example, a nitrile–guanosine substituted into thrombin aptamer DNA was found to undergo a large Stark shift from its monomeric absorption frequency.