Investigating the DNA-Binding Interactions of Small Organic Molecules Utilizing Ultrafast Nonlinear Spectroscopy.

Abstract

The DNA-binding mechanism of small organic molecules, such as DNA-targeted drugs and fluorescent nuclear dyes, is key to their performance. Therefore, understanding the DNA-binding mechanism is critical for the design and development of molecules targeted at DNA. The purpose of this present research is to investigate the DNA-binding interactions of small organic molecules by employing ultrafast nonlinear spectroscopy. While basic design principles are proposed, the DNA-binding modes of many small organic molecules cannot be unambiguously assigned based either on their structure, or through the use of many well-established spectroscopic techniques. A new methodology utilizing two-photon spectroscopy was developed to determine the DNA-binding modes of small organic molecules definitively, contrarily to other well-established spectroscopic techniques. The impact of this work is imbedded with the ultrafast nonlinear spectroscopic studies of the DNA-binding interactions of small organic molecules. The newly developed methodology demonstrated superior sensitivity at both low drug and DNA concentrations by more than order of magnitude in comparison to circular dichroism (CD). This indicates that our approach can be used to probe DNA-drug interactions at biologically relevant conditions, which is critical in drug research and development.

The impact of this work also investigated the DNA-binding interactions of newly synthesized fluorescent nuclear dyes. This study has led to the emergence of structure-property relationships of DNA-binding molecules that adopt a crescent or V-shaped scaffold. The findings reveal that the structure of these fluorophores can be designed to either intercalate or groove bind with DNA by structurally modifying the electron acceptor properties of the central heterocyclic core. This is important because it allows the performance, specificity, and localization of a DNA-binding molecule to be controlled. The localization and cellular uptake of these small molecules were evaluated by conducting a series of bio-imaging studies in live HeLa cells. This work is significant because the design strategy can be applied towards the development of small molecules aimed at DNA.