ArticleJournal of the American Chemical Society2013
The essential role of stacking adenines in a two-base-pair RNA kissing complex.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
- Article
- An A-rich linker between dengue virus tandem xrRNAs facilitates functional coordination.bioRxiv : the preprint server for biology · 2026Article
- Investigating Polarity Effects in DNA Base Stacking.JACS Au · 2025Article
- High-throughput single-molecule quantification of individual base stacking energies in nucleic acids.Nature communications · 2023Article
- Highly conserved s2m element of SARS-CoV-2 dimerizes via a kissing complex and interacts with host miRNA-1307-3p.Nucleic acids research · 2022Article
- Submicrometer Nanospray Emitters Provide New Insights into the Mechanism of Cation Adduction to Anionic Oligonucleotides.Analytical chemistry · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Direct and Topoisomerase II Mediated DNA Damage by Bis-3-chloropiperidines: The Importance of Being an Earnest G.ChemMedChem · 2017Article
- On the conformational stability of the smallest RNA kissing complexes maintained through two G·C base pairs.Biochemical and biophysical research communications · 2017Article
- Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry.The Analyst · 2016Article
- May the Best Molecule Win: Competition ESI Mass Spectrometry.International journal of molecular sciences · 2015Review
- Probing the structural dynamics of proteins and nucleic acids with optical tweezers.Current opinion in structural biology · 2015Review
- Construction of RNA-Quantum Dot Chimera for Nanoscale Resistive Biomemory Application.ACS nano · 2015Article
- Article
- Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.BMC bioinformatics · 2015Article
- Nanomanipulation of single RNA molecules by optical tweezers.Journal of visualized experiments : JoVE · 2014Article
- Many-body effect in ion binding to RNA.The Journal of chemical physics · 2014Article
- Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.RNA (New York, N.Y.) · 2014Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
In minimal RNA kissing complexes formed between hairpins with cognate GACG tetraloops, the two tertiary GC pairs are likely stabilized by the stacking of 5'-unpaired adenines at each end of the short helix. To test this hypothesis, we mutated the flanking adenines to various nucleosides and examined their effects on the kissing interaction. Electrospray ionization mass spectrometry was used to detect kissing dimers in a multiequilibria mixture, whereas optical tweezers were applied to monitor the (un)folding trajectories of single RNA molecules. The experimental findings were rationalized by molecular dynamics simulations. Together, the results showed that the stacked adenines are indispensable for the tertiary interaction. By shielding the tertiary base pairs from solvent and reducing their fraying, the stacked adenines made terminal pairs act more like interior base pairs. The purine double-ring of adenine was essential for effective stacking, whereas additional functional groups modulated the stabilizing effects through varying hydrophobic and electrostatic forces. Furthermore, formation of the kissing complex was dominated by base pairing, whereas its dissociation was significantly influenced by the flanking bases. Together, these findings indicate that unpaired flanking nucleotides play essential roles in the formation of otherwise unstable two-base-pair RNA tertiary interactions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.