ArticleProceedings of the National Academy of Sciences of the United States of America2022
Stem-loop formation drives RNA folding in mechanical unzipping experiments.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 37 citations in OpenAlex.
- Temperature-dependent funnel-like DNA folding landscapes.Nucleic acids research · 2025Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- Stick-slip unfolding favors self-association of expanded HTT mRNA.Nature communications · 2024Article
- Universal cold RNA phase transitions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Stick-slip unfolding favors self-association of expandedbioRxiv : the preprint server for biology · 2024Article
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- Temperature-dependent elastic properties of DNA.Biophysical reports · 2022Article
- Interdomain Linker Effect on the Mechanical Stability of Ig Domains in Titin.International journal of molecular sciences · 2022Article
- Measurement of the specific and non-specific binding energies of MgBiophysical journal · 2022Article
- Nucleic Acid Thermodynamics Derived from Mechanical Unzipping Experiments.Life (Basel, Switzerland) · 2022Review
- Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems.Entropy (Basel, Switzerland) · 2022Article
- Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods.QRB discovery · 2022Review
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3 authors at 2 institutions in 2 countries.
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Abstract
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force-distance curves (FDCs) exhibit strong irreversible effects with hysteresis and several intermediates, precluding the extraction of the NNBP energies with currently available methods. The combination of a suitable RNA synthesis with a tailored pulling protocol allowed us to obtain the fully reversible FDCs necessary to derive the NNBP energies. We demonstrate the equivalence of sodium and magnesium free-energy salt corrections at the level of individual NNBP. To characterize the irreversibility of the unzipping-rezipping process, we introduce a barrier energy landscape of the stem-loop structures forming along the complementary strands, which compete against the formation of the native hairpin. This landscape correlates with the hysteresis observed along the FDCs. RNA sequence analysis shows that base stacking and base pairing stabilize the stem-loops that kinetically trap the long-lived intermediates observed in the FDC. Stem-loops formation appears as a general mechanism to explain a wide range of behaviors observed in RNA folding.
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