ArticleJournal of the American Chemical Society2020
Duplex DNA Is Weakened in Nanoconfinement.
Article in Journal of the American Chemical Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 32 citations in OpenAlex.
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Dynamic Structures and Fast Transition Kinetics of Oxidized G-Quadruplexes.Small (Weinheim an der Bergstrasse, Germany) · 2024Article
- In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells.Nature communications · 2024Article
- Structure and Dynamics of dsDNA in Cell-like Environments.Entropy (Basel, Switzerland) · 2022Review
- Zeptoliter DNA Origami Reactor to Reveal Cosolute Effects on Nanoconfined G-Quadruplexes.The journal of physical chemistry letters · 2022Article
- Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes.Nucleic acids research · 2022Article
- Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement.Frontiers in chemistry · 2022Article
- DNA self-organization controls valence in programmable colloid design.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- DNA origami nano-mechanics.Chemical Society reviews · 2021Review
- Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy.Biomolecules · 2021Review
- Mechanical characterization of base analogue modified nucleic acids by force spectroscopy.Physical chemistry chemical physics : PCCP · 2021Article
- Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming aMolecules (Basel, Switzerland) · 2020Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
For proteins and DNA secondary structures such as G-quadruplexes and i-motifs, nanoconfinement can facilitate their folding and increase structural stabilities. However, the properties of the physiologically prevalent B-DNA duplex have not been elucidated inside the nanocavity. Using a 17-bp DNA duplex in the form of a hairpin stem, here, we probed folding and unfolding transitions of the hairpin DNA duplex inside a DNA origami nanocavity. Compared to the free solution, the DNA hairpin inside the nanocage with a 15 × 15 nm cross section showed a drastic decrease in mechanical (20 → 9 pN) and thermodynamic (25 → 6 kcal/mol) stabilities. Free energy profiles revealed that the activation energy of unzipping the hairpin DNA duplex decreased dramatically (28 → 8 kcal/mol), whereas the transition state moved closer to the unfolded state inside the nanocage. All of these indicate that nanoconfinement weakens the stability of the hairpin DNA duplex to an unexpected extent. In a DNA hairpin made of a stem that contains complementary telomeric G-quadruplex (GQ) and i-motif (iM) forming sequences, formation of the Hoogsteen base pairs underlining the GQ or iM is preferred over the Watson-Crick base pairs in the DNA hairpin. These results shed light on the behavior of DNA in nanochannels, nanopores, or nanopockets of various natural or synthetic machineries. It also elucidates an alternative pathway to populate noncanonical DNA over B-DNA in the cellular environment where the nanocavity is abundant.
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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.