ArticleNucleic acids research2020
Structure-guided DNA-DNA attraction mediated by divalent cations.
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 27 papers.
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Who cites it
27 citing papers in PubMed, 40 citations in OpenAlex.
- Imaging and mechanism of DNA-DNA recognition mediated by divalent ions.Nucleic acids research · 2026Article
- Translational Entropy-Driven Competitive and Additive Effects on DNA Higher-Order Structure via Ion Exchange Between Cations of Different Valencies.Entropy (Basel, Switzerland) · 2026Review
- Horseradish peroxidase assisted "signal-on" chemiluminescence aptasensor for sensitive detection of aflatoxin B1.RSC advances · 2026Article
- Local cation-clamping distorts and softens RNA duplex.Communications biology · 2026Article
- Helical correlations in curved DNA condensates.Nucleic acids research · 2025Article
- Insights on the binding mechanisms and structural dynamics of protamine-DNA interaction.Biophysical reviews · 2025Review
- BmNPV interacts with super-enhancer regions of the host chromatin to hijack cellular transcription machinery.Nucleic acids research · 2025Article
- Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations.Biomacromolecules · 2024Article
- Barium Concentration-Dependent Anomalous Electrophoresis of Synthetic DNA Motifs.ACS applied bio materials · 2024Article
- Article
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation.Biomacromolecules · 2024Article
- Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints.Nature communications · 2023Article
- Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions.Journal of chemical theory and computation · 2023Article
- Self-Assembly of DNA Nanostructures in Different Cations.Small (Weinheim an der Bergstrasse, Germany) · 2023Article
- Self-assembly of DNA nanostructures in different cations.bioRxiv : the preprint server for biology · 2023Article
- Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions.Langmuir : the ACS journal of surfaces and colloids · 2023Article
- Extracting and characterizing protein-free megabase-pair DNA forCell reports methods · 2022Article
- Regulation associated modules reflect 3D genome modularity associated with chromatin activity.Nature communications · 2022Article
- Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts.Science advances · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Probing the role of surface structure in electrostatic interactions, we report the first observation of sequence-dependent dsDNA condensation by divalent alkaline earth metal cations. Disparate behaviors were found between two repeating sequences with 100% AT content, a poly(A)-poly(T) duplex (AA-TT) and a poly(AT)-poly(TA) duplex (AT-TA). While AT-TA exhibits non-distinguishable behaviors from random-sequence genomic DNA, AA-TT condenses in all alkaline earth metal ions. We characterized these interactions experimentally and investigated the underlying principles using computer simulations. Both experiments and simulations demonstrate that AA-TT condensation is driven by non-specific ion-DNA interactions. Detailed analyses reveal sequence-enhanced major groove binding (SEGB) of point-charged alkali ions as the major difference between AA-TT and AT-TA, which originates from the continuous and close stacking of nucleobase partial charges. These SEGB cations elicit attraction via spatial juxtaposition with the phosphate backbone of neighboring helices, resulting in an azimuthal angular shift between apposing helices. Our study thus presents a distinct mechanism in which, sequence-directed surface motifs act with cations non-specifically to enact sequence-dependent behaviors. This physical insight allows a renewed understanding of the role of repeating sequences in genome organization and regulation and offers a facile approach for DNA technology to control the assembly process of nanostructures.
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