ArticleNucleic acids research2012
End-to-end attraction of duplex DNA.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes.Nature communications · 2026Article
- Polymeric Properties of Telomeric G-Quadruplex Multimers: Effects of Chemically Inert Crowders.Biomacromolecules · 2025Article
- A twist grain boundary phase in aqueous solutions of the nucleic acid tetramer GTAC.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport.Nature communications · 2024Article
- RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends.Journal of the American Chemical Society · 2024Article
- A computational model for structural dynamics and reconfiguration of DNA assemblies.Nature communications · 2023Article
- Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency.The journal of physical chemistry. B · 2023Article
- Stacking Interactions and Flexibility of Human Telomeric Multimers.Journal of the American Chemical Society · 2023Article
- The development of nucleic acids force fields: From an unchallenged past to a competitive future.Biophysical journal · 2023Review
- Non-enzymatic oligonucleotide ligation in coacervate protocells sustains compartment-content coupling.Nature communications · 2023Article
- Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions.Langmuir : the ACS journal of surfaces and colloids · 2023Article
- Homologous pairing in short double-stranded DNA-grafted colloidal microspheres.Biophysical journal · 2022Article
- Blunt-End Driven Re-entrant Ordering in Quasi Two-Dimensional Dispersions of Spherical DNA Brushes.ACS nano · 2022Article
- Mono- and bilayer smectic liquid crystal ordering in dense solutions of "gapped" DNA duplexes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- DNA Terminal-Specific Dispersion Behavior of Polystyrene Latex Microparticles Densely Covered with Oligo-DNA Strands Under High-Salt Conditions.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2021Article
- Chiral Systems Made from DNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- Controlling aggregation of cholesterol-modified DNA nanostructures.Nucleic acids research · 2019Article
- Free energy of conformational isomers: The case of gapped DNA duplexes.The European physical journal. E, Soft matter · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Nematic liquid crystals of bifunctional patchy spheres.The European physical journal. E, Soft matter · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276-1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5'-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.
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