Drug/DNA Interactions and Condensation Investigated with Atomic Force Microscopy

Abstract

Atomic force microscopy (AFM) is a particularly useful tool, for obtaining structural information about drug-nucleic acid interactions. The mode of drug binding intercalation versus groove binding can be determined from images acquired on individual DNA molecules as the length of a DNA molecule increases in direct proportion to the number of intercalators bound to it.

The efforts of this research were directed toward elucidating the mode of binding of a series of drugs based on polymers of naphthalenetetracarboxyl diimide (NDI) interacting with a linearized DNA plasmid. During the course of the investigation of these drugs, DNA intercalation was confirmed as the mode of binding and the binding affinity estimated. Unexpectedly, concentration-dependent formation of secondary DNA structures including condensates was observed. DNA toroids, spheres, and rods were imaged and measured. Conformations that are believed to be intermediate condensate forms were also identified at lower poly-NDI concentrations. Models for the DNA condensation process have been proposed.

Ultimately, this research furthers the understanding of DNA condensation which can be applied to gene delivery systems and anti-viral agents. It may also help direct the development of better drugs based on the insight of poly-intercalators interactions with DNA.