Understanding DNA interactions in crowded environments with a coarse-grained model
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Understanding DNA interactions in crowded environments with a coarse-grained model
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-10-02
DOI
10.1093/nar/gkaa854
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
- (2020) Erik Poppleton et al. NUCLEIC ACIDS RESEARCH
- An emergent understanding of strand displacement in RNA biology
- (2019) Fan Hong et al. JOURNAL OF STRUCTURAL BIOLOGY
- Force-Induced Unravelling of DNA Origami
- (2018) Megan C. Engel et al. ACS Nano
- Coarse-grained modelling of the structural properties of DNA origami
- (2018) Benedict E K Snodin et al. NUCLEIC ACIDS RESEARCH
- Predicting DNA hybridization kinetics from sequence
- (2017) Jinny X. Zhang et al. Nature Chemistry
- DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size
- (2017) Dinesh C Khara et al. NUCLEIC ACIDS RESEARCH
- DNA nanotechnology
- (2017) Nadrian C. Seeman et al. Nature Reviews Materials
- 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
- Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches
- (2016) Dmitriy Khodakov et al. ADVANCED DRUG DELIVERY REVIEWS
- Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal
- (2016) Aleks Reinhardt et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- Design principles for rapid folding of knotted DNA nanostructures
- (2016) Vid Kočar et al. Nature Communications
- 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
- Crowding-Induced Hybridization of Single DNA Hairpins
- (2015) Laura E. Baltierra-Jasso et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Structural imprints in vivo decode RNA regulatory mechanisms
- (2015) Robert C. Spitale 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
- Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size
- (2015) Jaeoh Shin et al. Soft Matter
- Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
- (2015) Christian Matek et al. Scientific Reports
- Connecting the Dots: The Effects of Macromolecular Crowding on Cell Physiology
- (2014) Márcio A. Mourão et al. BIOPHYSICAL JOURNAL
- The Role of Loop Stacking in the Dynamics of DNA Hairpin Formation
- (2014) Majid Mosayebi et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics
- (2014) N. F. Dupuis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids
- (2013) Shu-ichi Nakano et al. CHEMICAL REVIEWS
- Crowders Perturb the Entropy of RNA Energy Landscapes to Favor Folding
- (2013) Duncan Kilburn et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- 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
- Impact of macromolecular crowding on DNA replication
- (2013) Barak Akabayov et al. Nature Communications
- Sequence-dependent thermodynamics of a coarse-grained DNA model
- (2012) Petr Šulc et al. JOURNAL OF CHEMICAL PHYSICS
- Kinetics and Dynamics of DNA Hybridization
- (2011) Yandong Yin et al. ACCOUNTS OF CHEMICAL RESEARCH
- Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
- (2011) Thomas E. Ouldridge et al. JOURNAL OF CHEMICAL PHYSICS
- Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA
- (2011) Natalia A. Denesyuk et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Dynamic DNA nanotechnology using strand-displacement reactions
- (2011) David Yu Zhang et al. Nature Chemistry
- Challenges and opportunities for structural DNA nanotechnology
- (2011) Andre V. Pinheiro et al. Nature Nanotechnology
- Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability
- (2011) D. B. Knowles et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Extracting bulk properties of self-assembling systems from small simulations
- (2010) Thomas E Ouldridge et al. JOURNAL OF PHYSICS-CONDENSED MATTER
- Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect
- (2010) Duncan Kilburn et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences
- (2008) Huan-Xiang Zhou et al. Annual Review of Biophysics
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation