ArticleProceedings of the National Academy of Sciences of the United States of America2013
Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
- Long-stranded XNA-cssDNA hybrids for robust data storage.Science advances · 2026Article
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- Characterizing Complex Nucleic Acid Interactions of LINE1 ORF1p by Single-Molecule Force Spectroscopy.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics.Nucleic acids research · 2025Article
- TMPyP binding evokes a complex, tunable nanomechanical response in DNA.Nucleic acids research · 2024Article
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity.International journal of molecular sciences · 2024Article
- Tension Gauge Tethers as Tension Threshold and Duration Sensors.ACS sensors · 2023Article
- Temperature-dependent elastic properties of DNA.Biophysical reports · 2022Article
- Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA.Nucleic acids research · 2022Article
- Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation.Nucleic acids research · 2022Article
- Cisplatin fastens chromatin irreversibly even at a high chloride concentration.Nucleic acids research · 2021Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy.The journal of physical chemistry. B · 2021Article
- Optical manipulation: advances for biophotonics in the 21st century.Journal of biomedical optics · 2021Review
- Single-molecule calorimeter and free energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Chiral Systems Made from DNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Review
- Statistical mechanics of a double-stranded rod model for DNA melting and elasticity.Soft matter · 2020Article
6 more citing papers are in PubMed but not listed here.
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Abstract
Double-stranded DNA (dsDNA) unconstrained by torsion undergoes an overstretching transition at about 65 pN, elongating the DNA to about 1.7-fold. Three possible structural transitions have been debated for the nature of DNA overstretching: (i) "peeling" apart of dsDNA to produce a peeled ssDNA strand under tension while the other strand coils, (ii) "inside-strand separation" of dsDNA to two parallel ssDNA strands that share tension (melting bubbles), and (iii) "B-to-S" transition to a novel dsDNA, termed S-DNA. Here we overstretched an end-opened DNA (with one open end to allow peeling) and an end-closed (i.e., both ends of the linear DNA are covalently closed to prohibit peeling) and torsion-unconstrained DNA. We report that all three structural transitions exist depending on experimental conditions. For the end-opened DNA, the peeling transition and the B-to-S transition were observed; for the end-closed DNA, the inside-strand separation and the B-to-S transition were observed. The peeling transition and the inside-strand separation are hysteretic and have an entropy change of approximately 17 cal/(K⋅mol), whereas the B-to-S transition is nonhysteretic and has an entropy change of approximately -2 cal/(K⋅mol). The force-extension curves of peeled ssDNA, melting bubbles, and S-DNA were characterized by experiments. Our results provide experimental evidence for the formation of DNA melting bubbles driven by high tension and prove the existence of nonmelted S-DNA. Our findings afford a full understanding of three possible force-driven structural transitions of torsion-unconstrained DNA and the resulting three overstretched DNA structures.
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