Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView
Molecular simulation has become an integral part of the DNA/RNA nanotechnology
research pipeline. In particular, understanding the dynamics of structures and single …
research pipeline. In particular, understanding the dynamics of structures and single …
A primer on the oxDNA model of DNA: when to use it, how to simulate it and how to interpret the results
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology,
biophysics and nanotechnology. It is currently available via two independent open source …
biophysics and nanotechnology. It is currently available via two independent open source …
DNA-based programmable gate arrays for general-purpose DNA computing
The past decades have witnessed the evolution of electronic and photonic integrated
circuits, from application specific to programmable,. Although liquid-phase DNA circuitry …
circuits, from application specific to programmable,. Although liquid-phase DNA circuitry …
A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower
M Centola, E Poppleton, S Ray, M Centola… - Nature …, 2024 - nature.com
Molecular engineering seeks to create functional entities for modular use in the bottom-up
design of nanoassemblies that can perform complex tasks. Such systems require fuel …
design of nanoassemblies that can perform complex tasks. Such systems require fuel …
A reversibly gated protein-transporting membrane channel made of DNA
Controlled transport of biomolecules across lipid bilayer membranes is of profound
significance in biological processes. In cells, cargo exchange is mediated by dedicated …
significance in biological processes. In cells, cargo exchange is mediated by dedicated …
Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami
Wireframe DNA origami assemblies can now be programmed automatically from the top-
down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid …
down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid …
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology
software environment: the lack of both a fast and user-friendly visualization tool and a …
software environment: the lack of both a fast and user-friendly visualization tool and a …
A versatile DNA origami-based plasmonic nanoantenna for label-free single-molecule surface-enhanced Raman spectroscopy
DNA origami technology allows for the precise nanoscale assembly of chemical entities that
give rise to sophisticated functional materials. We have created a versatile DNA origami …
give rise to sophisticated functional materials. We have created a versatile DNA origami …
OxDNA. org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
E Poppleton, R Romero, A Mallya… - Nucleic acids …, 2021 - academic.oup.com
OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA
nanotechnology community to prototype, analyze and rationalize designed DNA and RNA …
nanotechnology community to prototype, analyze and rationalize designed DNA and RNA …
Environment‐dependent stability and mechanical properties of DNA origami six‐helix bundles with different crossover spacings
The internal design of DNA nanostructures defines how they behave in different
environmental conditions, such as endonuclease‐rich or low‐Mg2+ solutions. Notably, the …
environmental conditions, such as endonuclease‐rich or low‐Mg2+ solutions. Notably, the …