Solution‐Controlled Conformational Switching of an Anchored Wireframe DNA Nanostructure

Abstract

Self‐assembled DNA origami nanostructures have a high degree of programmable spatial control that enables nanoscale molecular manipulations. A surface‐tethered, flexible DNA nanomesh is reported herein which spontaneously undergoes sharp, dynamic conformational transitions under physiological conditions. The transitions occur between two major macrostates: a spread state dominated by the interaction between the DNA nanomesh and the BSA/streptavidin surface and a surface‐avoiding contracted state. Due to a slow rate of stochastic transition events on the order of tens of minutes, the dynamic conformations of individual structures can be detected in situ with DNA PAINT microscopy. Time series localization data with automated imaging processing to track the dynamically changing radial distribution of structural markers are combined. Conformational distributions of tethered structures in buffers with elevated pH exhibit a calcium‐dependent domination of the spread state. This is likely due to electrostatic interactions between the structures and immobilized surface proteins (BSA and streptavidin). An interaction is observed in solution under similar buffer conditions with dynamic light scattering. Exchanging between solutions that promote one or the other state leads to in situ sample‐wide transitions between the states. The technique herein can be a useful tool for dynamic control and observation of nanoscale interactions and spatial relationships.

A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

“…Another significant application area for oxDNA has been the simulation of large structures to assess their conformation, stability and flexibility ( Fernandez-Castanon et al, 2016 ; Schreck et al, 2016 ; Sharma et al, 2017 ; Shi et al, 2017 ; Benson et al, 2018 ; Choi et al, 2018 ; Coronel et al, 2018 ; Berengut et al, 2019 ; Brady et al, 2019 ; Hoffecker et al, 2019 ; Snodin et al, 2019 ; Berengut et al, 2020 ; Chhabra et al, 2020 ; Poppleton et al, 2020 ; Tortora et al, 2020 ; Yao et al, 2020 ).…”

A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results

“…Another significant application area for oxDNA has been the simulation of large structures to assess their conformation, stability and flexibility [30,52,[168][169][170][171][172][173][174][175][176][177][178][179][180][181].…”

Double‐ to Single‐Strand Transition Induces Forces and Motion in DNA Origami Nanostructures

“…Notably, several approaches have been developed to increase the response speed of dynamic DNA devices. On the other hand, external stimuli such as light, [ 35,36 ] temperature, [ 37 ] ions, [ 11,23 ] pH, [ 38–40 ] and electric fields [ 21,41 ] often enable much faster operation up to an increase in speed by many orders of magnitude. [ 41 ] For example, Karna et al.…”