ArticleNucleic acids research2008
Loop dependence of the stability and dynamics of nucleic acid hairpins.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 117 citations in OpenAlex.
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- Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model.Journal of biological physics · 2022Article
- The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex.Nucleic acids research · 2021Article
- Identification of an Aptamer With Binding Specificity to Tumor-Homing Myeloid-Derived Suppressor Cells.Frontiers in pharmacology · 2021Article
- Single-molecule fluorescence detection of a tricyclic nucleoside analogue.Chemical science · 2020Article
- A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures.Journal of the Royal Society, Interface · 2020Article
- Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer.Current research in structural biology · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Hairpin loops are critical to the formation of nucleic acid secondary structure, and to their function. Previous studies revealed a steep dependence of single-stranded DNA (ssDNA) hairpin stability with length of the loop (L) as approximately L(8.5 +/- 0.5), in 100 mM NaCl, which was attributed to intraloop stacking interactions. In this article, the loop-size dependence of RNA hairpin stabilities and their folding/unfolding kinetics were monitored with laser temperature-jump spectroscopy. Our results suggest that similar mechanisms stabilize small ssDNA and RNA loops, and show that salt contributes significantly to the dependence of hairpin stability on loop size. In 2.5 mM MgCl2, the stabilities of both ssDNA and RNA hairpins scale as approximately L(4 +/- 0.5), indicating that the intraloop interactions are weaker in the presence of Mg2+. Interestingly, the folding times for ssDNA hairpins (in 100 mM NaCl) and RNA hairpins (in 2.5 mM MgCl2) are similar despite differences in the salt conditions and the stem sequence, and increase similarly with loop size, approximately L(2.2 +/- 0.5) and approximately L(2.6 +/- 0.5), respectively. These results suggest that hairpins with small loops may be specifically stabilized by interactions of the Na+ ions with the loops. The results also reinforce the idea that folding times are dominated by an entropic search for the correct nucleating conformation.
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