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Single-Molecule Measurements of the Persistence Length of Double-Stranded RNA
Open accessAbstract
Over the past few years, it has become increasingly apparent that double-stranded RNA (dsRNA) plays a far greater role in the life cycle of a cell than previously expected. Numerous proteins, including helicases, polymerases, and nucleases interact specifically with the double helix of dsRNA. To understand the detailed nature of these dsRNA-protein interactions, the (bio)chemical, electrostatic, and mechanical properties of dsRNA need to be fully characterized. We present measurements of the persistence length of dsRNA using two different single-molecule techniques: magnetic tweezers and atomic force microscopy. We deduce a mean persistence length for long dsRNA molecules of 63.8 +/- 0.7 nm from force-extension measurements with the magnetic tweezers. We present atomic force microscopy images of dsRNA and demonstrate a new method for analyzing these, which yields an independent, yet consistent value of 62 +/- 2 nm for the persistence length. The introduction of these single-molecule techniques for dsRNA analysis opens the way for real-time, quantitative analysis of dsRNA-protein interactions.
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“long double-stranded RNA (dsRNA) is 10%–20% more elastic than double-stranded DNA (dsDNA)”
From Ribonucleotide errors, RNase HII, and ribonucleotide excision repair (2026) · cites this paper as Abels et al. 2005
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Metadata
- Authors
- Abels, J. A., Moreno-Herrero, F., van der Heijden, T., Dekker, C., & Dekker, N. H.
- Affiliations
- Delft University of Technology (NL)
- Corresponding author
- Dekker, N.H.
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 2005-04
- Volume
- 88
- Issue
- 4
- Pages
- 2737-2744
- ISSN
- 0006-3495 (ISSN-L)
- PMC
- PMC1305369
- OpenAlex
- W2163558891
- Cited by
- 269
- References
- 34
- Citations by year
- 2026: 9 · 2025: 15 · 2024: 15 · 2023: 9 · 2022: 20 · 2021: 11 · 2020: 12 · 2019: 8 · 2018: 22 · 2017: 13 · 2016: 19 · 2015: 13 · 2014: 16 · 2013: 11 · 2012: 12
- FWCI
- 6.76
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Biophysical Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Research Repository (Delft University of Technology) (submittedVersion)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- Topics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- double-stranded RNA, persistence length, magnetic tweezers, atomic force microscopy, helicase, nucleases, polymerase
- MeSH terms
- Biophysics, Buffers, DNA, Electrophoresis, Agar Gel, Kinetics, Magnetics, Models, Biological, Models, Theoretical, Protein Binding, RNA, DNA-Directed RNA Polymerases, RNA, Double-Stranded, Temperature, Transcription, Genetic, Viral Proteins, Models, Statistical, Polymerase Chain Reaction, Microscopy, Atomic Force, Ribonuclease III, Static Electricity
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