Characterizing the bending and flexibility induced by bulges in DNA duplexes

Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges

(2014) Anthony M. Mustoe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

From a structural average to the conformational ensemble of a DNA bulge

(2014) X. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT

(2014) R. Iinuma et al.   SCIENCE

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

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

The enabled state of DNA nanotechnology

(2013) Veikko Linko et al.   CURRENT OPINION IN BIOTECHNOLOGY

Coarse-grained simulations of DNA overstretching

(2013) Flavio Romano et al.   JOURNAL OF CHEMICAL PHYSICS

Approaching the Limit: Can One DNA Strand Assemble into Defined Nanostructures?

(2013) Cheng Tian et al.   LANGMUIR

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

On the biophysics and kinetics of toehold-mediated DNA strand displacement

(2013) Niranjan Srinivas et al.   NUCLEIC ACIDS RESEARCH

Strong bending of the DNA double helix

(2013) A. Vologodskii et al.   NUCLEIC ACIDS RESEARCH

Coarse-graining DNA for simulations of DNA nanotechnology

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

DNA Gridiron Nanostructures Based on Four-Arm Junctions

(2013) D. Han et al.   SCIENCE

Self-Assembly of DNA Nanotubes with Defined Diameters and Lengths

(2013) Hang Qian et al.   Small

Controlling the Chirality of DNA Nanocages

(2012) Chuan Zhang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Analysis of the Stability and Flexibility of RNA Complexes Containing Bulge Loops of Different Sizes

(2012) Boel Nyström Macchion et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The effect of topology on the structure and free energy landscape of DNA kissing complexes

(2012) Flavio Romano et al.   JOURNAL OF CHEMICAL PHYSICS

Sequence-dependent thermodynamics of a coarse-grained DNA model

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

DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism

(2012) Christian Matek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering

(2012) Adelene Y. L. Sim et al.   PHYSICAL REVIEW E

Three-Dimensional Structures Self-Assembled from DNA Bricks

(2012) Y. Ke et al.   SCIENCE

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation

(2011) Maximillian H Bailor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

3D maps of RNA interhelical junctions

(2011) Maximillian H Bailor et al.   Nature Protocols

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation

(2011) Anthony M. Mustoe et al.   NUCLEIC ACIDS RESEARCH

Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

(2011) H. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The radial distribution function of worm-like chains

(2010) N. B. Becker et al.   EUROPEAN PHYSICAL JOURNAL E

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

(2010) Thomas E. Ouldridge et al.   PHYSICAL REVIEW LETTERS

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

(2010) M. H. Bailor et al.   SCIENCE

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

DNA self-assembly: from 2D to 3D

(2009) Chuan Zhang et al.   FARADAY DISCUSSIONS

Analysis of Four-Way Junctions in RNA Structures

(2009) Christian Laing et al.   JOURNAL OF MOLECULAR BIOLOGY

Symmetry Controls the Face Geometry of DNA Polyhedra

(2009) Chuan Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

(2009) V. B. Chu et al.   RNA

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra

(2008) Yu He et al.   NATURE

Conformational flexibility facilitates self-assembly of complex DNA nanostructures

(2008) C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule FRET measures bends and kinks in DNA

(2008) A. K. Wozniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of collective motion in examples of coarsening and self-assembly

(2008) Stephen Whitelam et al.   Soft Matter