ArticleNucleic acids research2011
The ends of a large RNA molecule are necessarily close.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 66 citations in OpenAlex.
- Making Ends Meet or Just Meeting at the Ends? Assessing End-to-End Distance in Folded RNA Sequences and Other Branched Structures.Bulletin of mathematical biology · 2026Article
- LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits.Bioinformatics (Oxford, England) · 2026Article
- Ordered release of genomic RNA during icosahedral virus disassembly.Journal of virology · 2026Article
- Size control of lipid nanoparticles via simulation-based design of a microfluidic chip and its effect on mRNA delivery in vitro and in vivo.Journal of nanobiotechnology · 2025Article
- Dynamics and Regulation of mRNA Cap Recognition by Human eIF4F.bioRxiv : the preprint server for biology · 2025Article
- Conserved long-range interactions are required for stable folding of orthoflaviviral genomic RNA.Nucleic acids research · 2025Article
- Prediction of Circular RNA Secondary Structures and Their Targets.Advances in experimental medicine and biology · 2025Review
- The separation between mRNA-ends is more variable than expected.FEBS open bio · 2024Article
- Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.Macromolecular rapid communications · 2024Article
- Tailor made: the art of therapeutic mRNA design.Nature reviews. Drug discovery · 2024Review
- Interactions between terminal ribosomal RNA helices stabilize theRNA (New York, N.Y.) · 2023Article
- Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Single-molecule visualization of mRNA circularization during translation.Experimental & molecular medicine · 2023Review
- Linear-Time Algorithms for RNA Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Intrinsically Unstructured Sequences in the mRNA 3' UTR Reduce the Ability of Poly(A) Tail to Enhance Translation.Journal of molecular biology · 2022Article
- Single-chain models illustrate the 3D RNA folding shape during translation.Biophysical reports · 2022Article
- mRNA- and factor-driven dynamic variability controls eIF4F-cap recognition for translation initiation.Nucleic acids research · 2022Article
- Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics.Nature chemistry · 2022Article
- Thoughts on how to think (and talk) about RNA structure.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Making ends meet: New functions of mRNA secondary structure.Wiley interdisciplinary reviews. RNA · 2021Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We show on general theoretical grounds that the two ends of single-stranded (ss) RNA molecules (consisting of roughly equal proportions of A, C, G and U) are necessarily close together, largely independent of their length and sequence. This is demonstrated to be a direct consequence of two generic properties of the equilibrium secondary structures, namely that the average proportion of bases in pairs is ∼60% and that the average duplex length is ∼4. Based on mfold and Vienna computations on large numbers of ssRNAs of various lengths (1000-10 000 nt) and sequences (both random and biological), we find that the 5'-3' distance-defined as the sum of H-bond and covalent (ss) links separating the ends of the RNA chain-is small, averaging 15-20 for each set of viral sequences tested. For random sequences this distance is ∼12, consistent with the theory. We discuss the relevance of these results to evolved sequence complementarity and specific protein binding effects that are known to be important for keeping the two ends of viral and messenger RNAs in close proximity. Finally we speculate on how our conclusions imply indistinguishability in size and shape of equilibrated forms of linear and covalently circularized ssRNA molecules.
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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.