ArticleScientific reports2015
Determination of base binding strength and base stacking interaction of DNA duplex using atomic force microscope.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genomic sequence context differentially impacts stepwise oxidation by TET enzymes to shape DNA hydroxymethylation landscapes.Nucleic acids research · 2026Article
- A Generally Applicable Method for Disentangling the Effect of Individual Noncovalent Interactions on the Binding Energy.Angewandte Chemie (International ed. in English) · 2025Article
- Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing.Nature methods · 2023Article
- Inefficient uptake of small interfering RNAs is responsible for their inability to trigger RNA interference in Colorado potato beetle cells.Archives of insect biochemistry and physiology · 2023Article
- Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy.Nano letters · 2023Article
- Detecting Intact Virus Using Exogenous Oligonucleotide Labels.Analytical chemistry · 2022Article
- Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex.Chemical science · 2021Article
- Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.The journal of physical chemistry. B · 2021Article
- Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study.Molecules (Basel, Switzerland) · 2021Article
- Label-Free Oligonucleotide-Based SPR Biosensor for the Detection of the Gene Mutation Causing Prothrombin-Related Thrombophilia.Sensors (Basel, Switzerland) · 2020Article
- AnBio-protocol · 2020Article
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Authors and funding
4 authors.
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Abstract
As one of the most crucial properties of DNA, the structural stability and the mechanical strength are attracting a great attention. Here, we take advantage of high force resolution and high special resolution of Atom Force Microscope and investigate the mechanical force of DNA duplexes. To evaluate the base pair hydrogen bond strength and base stacking force in DNA strands, we designed two modes (unzipping and stretching) for the measurement rupture forces. Employing k-means clustering algorithm, the ruptured force are clustered and the mean values are estimated. We assessed the influence of experimental parameters and performed the force evaluation for DNA duplexes of pure dG/dC and dA/dT base pairs. The base binding strength of single dG/dC and single dA/dT were estimated to be 20.0 ± 0.2 pN and 14.0 ± 0.3 pN, respectively, and the base stacking interaction was estimated to be 2.0 ± 0.1 pN. Our results provide valuable information about the quantitative evaluation of the mechanical properties of the DNA duplexes.
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