Choice of fluorophore affects dynamic DNA nanostructures.

Kevin Jahnke,Maxim Igaev,Kerstin Göpfrich,Helmut Grubmüller

doi:10.1093/nar/gkab201

Abstract

The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modelling, we demonstrate for 12 different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation—without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.

Highlights

DNA nanotechnology has been highly successful in repurposing the iconic DNA double helix to create programmable molecular architectures
In contrast to Förster Resonance Energy Transfer (FRET), which is commonly employed to monitor the pH dynamics, [21] our system provides freedom regarding the choice of fluorophores – which is absolutely necessary for us to study the impact of different fluorophore combinations
One of the most exciting tasks in the field of DNA nanotechnology is the construction of dynamic molecular devices that can perform mechanical motion upon stimulation

Summary

Introduction

DNA nanotechnology has been highly successful in repurposing the iconic DNA double helix to create programmable molecular architectures. Once focused on static shapes, dynamic and stimuli-responsive DNA nanoscale devices are gaining a large surge of interest for various applications [1] – from sensors, [2,3,4] biocomputing algorithms, [5] and drug delivery systems [6,7] to programmable robotic modules [8,9] and functional components for synthetic cells. [4,18] The ability to reversibly actuate artificial structures at the nanoscale is at the core of dynamic DNA nanotechnology. The use of fluorescent dyes is commonplace to validate and quantify the functionality of the DNA-based devices. We show that the choice of the fluorophore itself can alter the equilibrium conformation and even inhibit a desired dynamic response.

Methods

Results

Conclusion