ArticleNucleic acids research2010
Differential stability of DNA crossovers in solution mediated by divalent cations.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 50 citations in OpenAlex.
- Biomolecular and cellular chirality: Novel diagnostic perspectives for diseases.APL bioengineering · 2026Review
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.The journal of physical chemistry. B · 2023Article
- Article
- The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.Nature communications · 2022Article
- Article
- Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes.RSC advances · 2022Article
- Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.Nucleic acids research · 2022Article
- Towards the Idea of Molecular Brains.International journal of molecular sciences · 2021Review
- Ion-mediated interactions between like-charged polyelectrolytes with bending flexibility.Scientific reports · 2020Article
- Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States.Scientific reports · 2018Article
- Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex.Biophysical journal · 2017Article
- The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity.Biophysical reviews · 2016Review
- A metastable structure for the compact 30-nm chromatin fibre.FEBS letters · 2016Article
- Protein/DNA interactions in complex DNA topologies: expect the unexpected.Biophysical reviews · 2016Review
- Protein/DNA interactions in complex DNA topologies: expect the unexpected.Biophysical reviews · 2016Review
- Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA.Nucleic acids research · 2015Article
- Determination of base binding strength and base stacking interaction of DNA duplex using atomic force microscope.Scientific reports · 2015Article
- DNA self-assembly: from chirality to evolution.International journal of molecular sciences · 2013Review
- DNA-directed base pair opening.Molecules (Basel, Switzerland) · 2012Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The assembly of DNA duplexes into higher-order structures plays a major role in many vital cellular functions such as recombination, chromatin packaging and gene regulation. However, little is currently known about the molecular structure and stability of direct DNA-DNA interactions that are required for such functions. In nature, DNA helices minimize electrostatic repulsion between double helices in several ways. Within crystals, B-DNA forms either right-handed crossovers by groove-backbone interaction or left-handed crossovers by groove-groove juxtaposition. We evaluated the stability of such crossovers at various ionic concentrations using large-scale atomistic molecular dynamics simulations. Our results show that right-handed DNA crossovers are thermodynamically stable in solution in the presence of divalent cations. Attractive forces at short-range stabilize such crossover structures with inter-axial separation of helices less than 20 A. Right-handed crossovers, however, dissociate swiftly in the presence of monovalent ions only. Surprisingly, left-handed crossovers, assembled by sequence-independent juxtaposition of the helices, appear unstable even at the highest concentration of Mg(2+)studied here. Our study provides new molecular insights into chiral association of DNA duplexes and highlights the unique role divalent cations play in differential stabilization of crossover structures. These results may serve as a rational basis to understand the role DNA crossovers play in biological processes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.