ArticleNucleic acids research2020
Understanding DNA interactions in crowded environments with a coarse-grained model.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 36 citations in OpenAlex.
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- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Ministring DNA (msDNA): a novel linear covalently-closed DNA with enhanced stability for gene and cell therapy applications.Scientific reports · 2025Article
- Influence of Media Disorder on DNA Melting: A Monte Carlo Study.Journal of chemical theory and computation · 2025Article
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- Molecular Compressive Force Sensor for Mapping Forces at the Cell-Substrate Interface.Journal of the American Chemical Society · 2024Article
- Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers.Entropy (Basel, Switzerland) · 2023Article
- Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.International journal of molecular sciences · 2022Article
- Structure and Dynamics of dsDNA in Cell-like Environments.Entropy (Basel, Switzerland) · 2022Review
- Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions.PLoS computational biology · 2022Article
- Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding.International journal of molecular sciences · 2022Article
- OxDNA to Study Species Interactions.Entropy (Basel, Switzerland) · 2022Article
- Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems.Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology · 2022Review
- Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection.Exploration (Beijing, China) · 2022Article
- Aqueous Triple-Phase System in Microwell Array for Generating Uniform-Sized DNA Hydrogel Particles.Frontiers in genetics · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology.
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Registered trials
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