ArticleBiophysical journal2006
Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Efficient non-viral immune cell engineering using circular single-stranded DNA-mediated genomic integration.Nature biotechnology · 2025Article
- Preparation of topoisomers of short circular dsDNA with defined linking number by accurate topological control.Nucleic acids research · 2025Article
- Direct dsRNA preparation by promoter-free RCT and RNase H cleavage using one circular dsDNA template with a mismatched bubble.RNA (New York, N.Y.) · 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
- Conformational Dynamics of Poly(T) Single-Stranded DNA at the Single-Molecule Level.The journal of physical chemistry letters · 2021Article
- Facile Characterization of Topology of DNA Catenanes.Biophysical journal · 2020Article
- Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.Journal of chemical theory and computation · 2019Article
- Terminal hairpin in oligonucleotide dominantly prioritizes intramolecular cyclization by T4 ligase over intermolecular polymerization: an exclusive methodology for producing ssDNA rings.Nucleic acids research · 2018Article
- Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane.Molecules (Basel, Switzerland) · 2018Article
- Modeling protein folding in vivo.Biology direct · 2018Article
- Cyclization of secondarily structured oligonucleotides to single-stranded rings by usingRSC advances · 2018Article
- Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration.Nucleic acids research · 2017Article
- JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.PloS one · 2017Article
- The role of the backbone torsion in protein folding.Biology direct · 2016Article
- Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore.Beilstein journal of nanotechnology · 2016Article
- Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics.The journal of physical chemistry. B · 2014Article
- Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions.Nucleic acids research · 2014Article
- Article
- Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.Journal of molecular biology · 2009Article
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Authors and funding
3 authors.
Funding
Abstract
Single-stranded DNA (ssDNA) has essential biological functions during DNA replication, recombination, repair, and transcription. The structure of ssDNA must be better understood to elucidate its functions. However, the available data are too limited to give a clear picture of ssDNA due to the extremely capricious structural features of ssDNA. In this study, by forming DNA catenanes and determining their topology (the linking number, Lk) through the electrophoretic analysis, we demonstrate that the studies of catenanes formed from two ssDNA molecules can yield valuable new information about the ssDNA secondary structure. We construct catenanes out of two short (60/70 nt) ssDNA molecules by enzymatic cyclization of linear oligodeoxynucleotides. The secondary structure formed between the two DNA circles determines the topology (the Lk value) of the constructed DNA catenane. Thus, formation of the secondary structure is experimentally monitored by observing the changes of linking number with sequences and conditions. We found that the secondary structure of ssDNA is much easier to form than expected: the two strands in an internal loop in the folded ssDNA structure prefer to braid around each other rather than stay separately forming a loop, and a duplex containing only mismatched basepairs can form under physiological conditions.
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