Structure and conformational dynamics of scaffolded DNA origami nanoparticles
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Title
Structure and conformational dynamics of scaffolded DNA origami nanoparticles
Authors
Keywords
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Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue 11, Pages 6284-6298
Publisher
Oxford University Press (OUP)
Online
2017-04-25
DOI
10.1093/nar/gkx378
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Related references
Note: Only part of the references are listed.- Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model
- (2016) John S. Schreck et al. ACS Nano
- Direct Simulation of the Self-Assembly of a Small DNA Origami
- (2016) Benedict E. K. Snodin et al. ACS Nano
- Multiscale simulation of DNA
- (2016) Pablo D Dans et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
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- (2016) Christopher Maffeo et al. NUCLEIC ACIDS RESEARCH
- Designer nanoscale DNA assemblies programmed from the top down
- (2016) R. Veneziano et al. SCIENCE
- Characterizing the bending and flexibility induced by bulges in DNA duplexes
- (2015) John S. Schreck 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
- Martini Coarse-Grained Force Field: Extension to DNA
- (2015) Jaakko J. Uusitalo et al. Journal of Chemical Theory and Computation
- Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies
- (2015) Reza Sharifi Sedeh et al. Journal of Chemical Theory and Computation
- A coarse-grained MARTINI-like force field for DNA unzipping in nanopores
- (2015) Anna Stachiewicz et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- DNA rendering of polyhedral meshes at the nanoscale
- (2015) Erik Benson et al. NATURE
- Guiding the folding pathway of DNA origami
- (2015) Katherine E. Dunn et al. NATURE
- Complex wireframe DNA origami nanostructures with multi-arm junction vertices
- (2015) Fei Zhang et al. Nature Nanotechnology
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
- (2014) Fabio Sterpone et al. CHEMICAL SOCIETY REVIEWS
- A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method
- (2014) Aymeric Naômé et al. Journal of Chemical Theory and Computation
- A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment
- (2014) Christopher Maffeo et al. Journal of Chemical Theory and Computation
- Structural DNA Nanotechnology: State of the Art and Future Perspective
- (2014) Fei Zhang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT
- (2014) R. Iinuma et al. SCIENCE
- Casting inorganic structures with DNA molds
- (2014) W. Sun et al. SCIENCE
- Lattice-free prediction of three-dimensional structure of programmed DNA assemblies
- (2014) Keyao Pan et al. Nature Communications
- A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo
- (2014) Nikolay Korolev et al. Polymers
- Coarse-Graining Methods for Computational Biology
- (2013) Marissa G. Saunders et al. Annual Review of Biophysics
- Perspective on the Martini model
- (2013) Siewert J. Marrink et al. CHEMICAL SOCIETY REVIEWS
- Coarse-grained simulations of DNA overstretching
- (2013) Flavio Romano et al. JOURNAL OF CHEMICAL PHYSICS
- 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
- Perspective: Coarse-grained models for biomolecular systems
- (2013) W. G. Noid JOURNAL OF CHEMICAL PHYSICS
- Coarse-Grained Simulations of RNA and DNA Duplexes
- (2013) Tristan Cragnolini et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame
- (2013) A. Rajendran et al. NUCLEIC ACIDS RESEARCH
- DNA hybridization kinetics: zippering, internal displacement and sequence dependence
- (2013) Thomas E. Ouldridge et al. NUCLEIC ACIDS RESEARCH
- Structure-based model for light-harvesting properties of nucleic acid nanostructures
- (2013) Keyao Pan et al. NUCLEIC ACIDS RESEARCH
- Coarse-graining DNA for simulations of DNA nanotechnology
- (2013) Jonathan P. K. Doye et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
- (2013) J. Yoo et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DNA Gridiron Nanostructures Based on Four-Arm Junctions
- (2013) D. Han et al. SCIENCE
- Triplex-Directed Recognition of a DNA Nanostructure Assembled by Crossover Strand Exchange
- (2012) David A. Rusling et al. ACS Nano
- Coarse-graining of multiprotein assemblies
- (2012) Marissa G Saunders et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Modeling nucleic acids
- (2012) Adelene YL Sim et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations
- (2012) Olof Allnér et al. Journal of Chemical Theory and Computation
- A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads
- (2012) S. M. Douglas et al. SCIENCE
- Recent successes in coarse-grained modeling of DNA
- (2012) Davit A. Potoyan et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Frontiers in Molecular Dynamics Simulations of DNA
- (2011) Alberto Pérez et al. ACCOUNTS OF CHEMICAL RESEARCH
- Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites
- (2011) Juan J. de Pablo Annual Review of Physical Chemistry
- ProDy: Protein Dynamics Inferred from Theory and Experiments
- (2011) A. Bakan et al. BIOINFORMATICS
- Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
- (2011) Katarina Hart et al. Journal of Chemical Theory and Computation
- Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
- (2011) Elizabeth J. Denning et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Multilayer DNA Origami Packed on Hexagonal and Hybrid Lattices
- (2011) Yonggang Ke et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Dynamic DNA nanotechnology using strand-displacement reactions
- (2011) David Yu Zhang et al. Nature Chemistry
- 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
- Coarse-grained force field: general folding theory
- (2011) Adam Liwo et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- DNA Origami with Complex Curvatures in Three-Dimensional Space
- (2011) D. Han et al. SCIENCE
- Nanomaterials Based on DNA
- (2010) Nadrian C. Seeman Annual Review of Biochemistry
- A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
- (2010) Alex Morriss-Andrews et al. JOURNAL OF CHEMICAL PHYSICS
- A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics
- (2010) Pablo D. Dans et al. Journal of Chemical Theory and Computation
- A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions
- (2010) Robert C. DeMille et al. JOURNAL OF PHYSICAL CHEMISTRY B
- DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
- (2010) Thomas E. Ouldridge et al. PHYSICAL REVIEW LETTERS
- Chemically accurate coarse graining of double-stranded DNA
- (2010) A. Savelyev et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2009) Yonggang Ke et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Nanofabrication by DNA self-assembly
- (2009) Hanying Li et al. Materials Today
- Self-assembly of DNA into nanoscale three-dimensional shapes
- (2009) Shawn M. Douglas et al. NATURE
- From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal
- (2009) Jianping Zheng et al. NATURE
- Self-assembly of a nanoscale DNA box with a controllable lid
- (2009) Ebbe S. Andersen 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
- DNA and lipid bilayers: self-assembly and insertion
- (2008) S. Khalid et al. Journal of the Royal Society Interface
- Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
- (2008) Yu He et al. NATURE
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