ArticleThe journal of physical chemistry. B2023
Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency.
Article in The journal of physical chemistry. B, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed, 7 citations in OpenAlex.
- Low-Energy Electron Scattering from 2‑Butyne: Elastic and Electronic Excitation Processes.ACS omega · 2026Article
- Imaging and mechanism of DNA-DNA recognition mediated by divalent ions.Nucleic acids research · 2026Article
- Ion-Specific Modulation of the Conformation and Compactness of DNA Oligo-Catenanes.The journal of physical chemistry. B · 2026Article
- Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.bioRxiv : the preprint server for biology · 2024Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles. This can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending due to the presence of free ends.
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Registered trials
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.