ArticleThe journal of physical chemistry letters2021
Conformational Dynamics of Poly(T) Single-Stranded DNA at the Single-Molecule Level.
Article in The journal of physical chemistry letters, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 18 citations in OpenAlex.
- Three-color single-molecule fluorescence resonance energy transfer to study macromolecular dynamics.Current opinion in structural biology · 2026Review
- A 3D-Printed Scaffolded Hydrogel Microneedle Array Biosensor for Real-Time, Continuous Monitoring.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Human hnRNPA1 reorganizes telomere-bound replication protein A.Nucleic acids research · 2024Article
- Replication of [AT/TA]Biochemistry · 2024Article
- Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions.Journal of molecular biology · 2024Article
- Replication of [AT/TA]bioRxiv : the preprint server for biology · 2023Article
- Circular single-stranded DNA as switchable vector for gene expression in mammalian cells.Nature communications · 2023Article
- DNA Volume, Topology, and Flexibility Dictate Nanopore Current Signals.Nano letters · 2023Article
- Molecular DNA dendron vaccines.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Discrete RNA-DNA hybrid cleavage by the EXD2 exonuclease pinpoints two rate-limiting steps.The EMBO journal · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The conformational dynamics of single-stranded DNA (ss-DNA) are implicated in the mechanisms of several key biological processes such as DNA replication and damage repair and have been modeled with those of semiflexible or flexible polymer. The high flexibility and customizability of ss-DNA also make it an excellent polymeric material for materials engineering. Polythymidine (poly(T)) is an excellent model ss-DNA as a flexible polymer since it does not form any secondary structure. However, only limited experimental results have been reported of poly(T) conformational dynamics with a very short length that is not relevant to the aforementioned processes and applications. Here, we provide the first experimental results of the conformational dynamics of poly(T) with lengths in the range of 130-170 nucleotides at the single-molecule level. Our experiments are based on single-molecule FRET and a DNA hairpin structure of which the folding kinetics are governed by the conformational dynamics of poly(T). We found that the folding kinetics deviate far from those of a flexible polymer model with a harmonic bending potential. To this end, we derived a simple model for the kinetics of DNA hairpin folding from the self-avoiding-walk (SAW). Our model describes the conformational dynamics of poly(T) very well and enables estimation of the conformational dimensionality. The estimated dimensionalities suggest that ss-DNA is completely flexible at 100 mM or a higher NaCl concentration, but not at 50 mM. These results will help understand the conformational dynamics of ss-DNA implicated in several key biological processes and maximize the utility of ss-DNA for materials engineering. Also, our system and model provide an excellent platform to investigate the conformational dynamics of ss-DNA.
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