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, 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 …

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 …

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 …

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 …

RNA origami: design, simulation and application

E Poppleton, N Urbanek, T Chakraborty, A Griffo… - RNA biology, 2023 - Taylor & Francis
Design strategies for DNA and RNA nanostructures have developed along parallel lines for
the past 30 years, from small structural motifs derived from biology to large …

Modulating lipid membrane morphology by dynamic DNA origami networks

J Yang, K Jahnke, L **n, X **g, P Zhan, A Peil… - Nano Letters, 2023 - ACS Publications
Membrane morphology and its dynamic adaptation regulate many cellular functions, which
are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled …

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

D Hayakawa, TE Videbaek, DM Hall… - Proceedings of the …, 2022 - National Acad Sciences
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 …

Planar 2D wireframe DNA origami

X Wang, S Li, H Jun, T John, K Zhang, H Fowler… - Science …, 2022 - science.org
Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics
to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility …

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 …