Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites

TL;DR

This study investigates how the structure of DNA origami nanostructures affects drug intercalation, revealing that not all binding sites are accessible, which impacts their design for targeted drug delivery.

Contribution

The paper provides the first detailed biophysical analysis of intercalation site accessibility in DNA origami nanostructures, highlighting structural limitations for drug loading.

Findings

Not all potential intercalation sites are accessible in DNA origami.

Biophysical techniques reveal structural inaccessibility impacts drug loading.

Results inform future design of DNA nanostructures for drug delivery.

Abstract

Intercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.