ArticleNucleic acids research2007
Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 53 citations in OpenAlex.
- Exploring the Application of Nano-Differential Scanning Calorimetry in RNA Characterization.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Capillary Electrophoresis Can Detect the Simultaneous Presence of Hairpins and Self-Dimers in Non-Symmetric, Single-Stranded DNA Oligomers.Electrophoresis · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes.The journal of physical chemistry. B · 2024Article
- Polycations as Aptamer-Binding Modulators for Sensitive Fluorescence Anisotropy Assay of Aflatoxin B1.Sensors (Basel, Switzerland) · 2024Article
- Directed Circularization of a Short RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides.International journal of molecular sciences · 2023Article
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- Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.Algorithms for molecular biology : AMB · 2023Article
- DNA Materials Assembled from One DNA Strand.International journal of molecular sciences · 2023Review
- RNA granules: functional compartments or incidental condensates?Genes & development · 2023Review
- RNA sequence and structure control assembly and function of RNA condensates.RNA (New York, N.Y.) · 2021Article
- Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition.Nucleic acids research · 2019Article
- Article
- 1.25 Å resolution structure of an RNA 20-mer that binds to the TREX2 complex.Acta crystallographica. Section F, Structural biology communications · 2015Article
- Master sensors of pathogenic RNA - RIG-I like receptors.Immunobiology · 2013Review
- Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site.Nucleic acids research · 2011Article
- RNA dimerization monitored by fluorescence correlation spectroscopy.European biophysics journal : EBJ · 2011Article
- Crystallization and preliminary X-ray diffraction analysis of a self-complementary DNA heptacosamer with a 20-base-pair duplex flanked by seven-nucleotide overhangs at the 3'-terminus.Acta crystallographica. Section F, Structural biology and crystallization communications · 2010Article
- What drives the binding of minor groove-directed ligands to DNA hairpins?Nucleic acids research · 2008Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A self-complementary nucleotide sequence can form both a unimolecular hairpin and a bimolecular duplex. In this study, the secondary structures of the self-complementary DNA and RNA oligonucleotides with different sequences and lengths were investigated under various solution conditions by gel electrophoresis, circular dichroism (CD) and electron paramagnetic resonance (EPR) spectroscopy and a ultraviolet (UV) melting analysis. The DNA sequences tended to adopt a hairpin conformation at low cation concentrations, but a bimolecular duplex was preferentially formed at an elevated cationic strength. On the other hand, fully matched RNA sequences adopted a bimolecular duplex regardless of the cation concentration. The thermal melting experiments indicated a greater change in the melting temperature of the bimolecular duplexes (by approximately 20 degrees C) than that of the hairpin (by approximately 10 degrees C) by increasing the NaCl concentration from 10 mM to 1 M. Hairpin formations were also observed for the palindrome DNA sequences derived from Escherichia coli, but association of the complementary palindrome sequences was observed when spermine, one of the major cationic molecules in a cell, existed at the physiological concentration. The results indicate the role of cations for shifting the structural equilibrium toward a nucleotide assembly and implicate nucleotide structures in cells.
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