Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView

J Bohlin, M Matthies, E Poppleton, J Procyk, A Mallya… - Nature protocols, 2022 - nature.com
Molecular simulation has become an integral part of the DNA/RNA nanotechnology
research pipeline. In particular, understanding the dynamics of structures and single …

Designer nanomaterials through programmable assembly

JS Kahn, O Gang - Angewandte Chemie International Edition, 2022 - Wiley Online Library
Nanoparticles have long been recognized for their unique properties, leading to exciting
potential applications across optics, electronics, magnetism, and catalysis. These specific …

Prediction of DNA origami shape using graph neural network

C Truong-Quoc, JY Lee, KS Kim, DN Kim - Nature Materials, 2024 - nature.com
Unlike proteins, which have a wealth of validated structural data, experimentally or
computationally validated DNA origami datasets are limited. Here we present a graph neural …

A DNA turbine powered by a transmembrane potential across a nanopore

X Shi, AK Pumm, C Maffeo, F Kohler, E Feigl… - Nature …, 2024 - nature.com
Rotary motors play key roles in energy transduction, from macroscale windmills to
nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines …

3D RNA-scaffolded wireframe origami

MF Parsons, MF Allan, S Li, TR Shepherd… - Nature …, 2023 - nature.com
Hybrid RNA: DNA origami, in which a long RNA scaffold strand folds into a target
nanostructure via thermal annealing with complementary DNA oligos, has only been …

Designing Rigid DNA Origami Templates for Molecular Visualization Using Cryo-EM

A Khoshouei, G Kempf, V Mykhailiuk, JM Griessing… - Nano Letters, 2024 - ACS Publications
DNA origami, a method for constructing nanostructures from DNA, offers potential for diverse
scientific and technological applications due to its ability to integrate various molecular …

Geometrically programmed self-limited assembly of tubules using DNA origami colloids

D Hayakawa, TE Videbaek, DM Hall, H Fang… - Proceedings of the …, 2022 - pnas.org
Self-assembly is one of the most promising strategies for making functional materials at the
nanoscale, yet new design principles for making self-limiting architectures, rather than …

A computational model for structural dynamics and reconfiguration of DNA assemblies

JY Lee, H Koh, DN Kim - Nature Communications, 2023 - nature.com
Recent advances in constructing a structured DNA assembly whose configuration can be
dynamically changed in response to external stimuli have demanded the development of an …

DNA origami traps for large viruses

A Monferrer, F Kohler, C Sigl, M Schachtner… - Cell Reports Physical …, 2023 - cell.com
Virus-envelo** macromolecular shells or tilings can prevent viruses from entering cells.
Here, we describe the design and assembly of a cone-shaped DNA origami higher-order …

Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations

K Ahmad, A Javed, C Lanphere, PV Coveney… - Nature …, 2023 - nature.com
DNA can be folded into rationally designed, unique, and functional materials. To fully realise
the potential of these DNA materials, a fundamental understanding of their structure and …