Use of UV-Vis Spectrometry to Gain Information on the Mode of Binding of Small Molecules to DNAs and RNAs

Ultraviolet-visible (UV-Vis) spectrometries (absorbance, linear dichroism [LD], and circular dichroism [CD]) are relatively simple techniques that can provide important information on the mode of binding of small molecules (dyes, drugs) to DNA and RNA helices. In this article the spectral characteristics of three families of dyes upon interaction with polynucleotides are reviewed. Each of them is representative for one of the major binding modes: acridines for intercalation, Hoechst dyes for groove binding, and porphyrins for external dye stacking. The purpose is to help the reader who is not accustomed to using these systems to gain a simple picture of what the predominant UV-Vis features of each binding mode are. These data are discussed and tables are provided to collect and compare the absorbance, LD, and CD spectral features of several examples of the three dye families chosen.