Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation

Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure

(2020) Antonio Suma et al.   NUCLEIC ACIDS RESEARCH

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

(2020) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Autonomously designed free-form 2D DNA origami

(2019) Hyungmin Jun et al.   Science Advances

TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami

(2019) Antonio Suma et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering

(2018) Matthew A. B. Baker et al.   ACS Nano

Force-Induced Unravelling of DNA Origami

(2018) Megan C. Engel et al.   ACS Nano

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

(2018) Pedro Fonseca et al.   JOURNAL OF CHEMICAL PHYSICS

A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo

(2018) Suping Li et al.   NATURE BIOTECHNOLOGY

Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices

(2018) Matthias Schickinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering

(2018) Fan Hong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Coarse-grained modelling of the structural properties of DNA origami

(2018) Benedict E K Snodin et al.   NUCLEIC ACIDS RESEARCH

Programming molecular topologies from single-stranded nucleic acids

(2018) Xiaodong Qi et al.   Nature Communications

Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns

(2017) Grigory Tikhomirov et al.   NATURE

Single-stranded DNA and RNA origami

(2017) Dongran Han et al.   SCIENCE

Direct Simulation of the Self-Assembly of a Small DNA Origami

(2016) Benedict E. K. Snodin et al.   ACS Nano

Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes

(2016) Erik Benson et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Engineering and mapping nanocavity emission via precision placement of DNA origami

(2016) Ashwin Gopinath et al.   NATURE

De novoreconstruction of DNA origami structures through atomistic molecular dynamics simulation

(2016) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Designer nanoscale DNA assemblies programmed from the top down

(2016) R. Veneziano et al.   SCIENCE

Coarse-grained modelling of supercoiled RNA

(2015) Christian Matek et al.   JOURNAL OF CHEMICAL PHYSICS

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

(2015) Benedict E. K. Snodin et al.   JOURNAL OF CHEMICAL PHYSICS

DNA rendering of polyhedral meshes at the nanoscale

(2015) Erik Benson et al.   NATURE

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

(2015) John S. Schreck et al.   NUCLEIC ACIDS RESEARCH

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

(2015) T. Gerling et al.   SCIENCE

A nucleotide-level coarse-grained model of RNA

(2014) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Numerical Evidence for Nucleated Self-Assembly of DNA Brick Structures

(2014) Aleks Reinhardt et al.   PHYSICAL REVIEW LETTERS

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

(2013) Thomas E. Ouldridge et al.   ACS Nano

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

(2013) Daniel M. Hinckley et al.   JOURNAL OF CHEMICAL PHYSICS

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

(2013) Petr Šulc et al.   Natural Computing

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

(2013) Thomas E. Ouldridge et al.   NUCLEIC ACIDS RESEARCH

Coarse-graining DNA for simulations of DNA nanotechnology

(2013) Jonathan P. K. Doye et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Complex shapes self-assembled from single-stranded DNA tiles

(2012) Bryan Wei et al.   NATURE

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

A primer to scaffolded DNA origami

(2011) Carlos Ernesto Castro et al.   NATURE METHODS

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

(2011) Do-Nyun Kim et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

Rapid prototyping of 3D DNA-origami shapes with caDNAno

(2009) Shawn M. Douglas et al.   NUCLEIC ACIDS RESEARCH

Folding DNA into Twisted and Curved Nanoscale Shapes

(2009) H. Dietz et al.   SCIENCE