ArticleProceedings of the National Academy of Sciences of the United States of America2008
Predicting the sizes of large RNA molecules.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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82 citing papers in PubMed.
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- A Nonviral Neo-Nucleocapsid for Cell-Specific RNA Delivery Developed by Pseudo-Cyclic Peptide Grafting and Directed Evolution.Angewandte Chemie (International ed. in English) · 2026Article
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- Measuring the selective packaging of RNA molecules by viral coat proteins in cells.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Conserved long-range interactions are required for stable folding of orthoflaviviral genomic RNA.Nucleic acids research · 2025Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.Macromolecular rapid communications · 2024Article
- Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA.Biophysical journal · 2024Article
- Pioneering role of RNA in the early evolution of life.Genetics and molecular biology · 2024Article
- Long ssRNA undergoes continuous compaction in the presence of polyvalent cations.Biophysical journal · 2023Article
- Single-chain models illustrate the 3D RNA folding shape during translation.Biophysical reports · 2022Article
- Packaging contests between viral RNA molecules and kinetic selectivity.PLoS computational biology · 2022Article
- Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics.Nature communications · 2022Article
- What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?RNA (New York, N.Y.) · 2022Review
- Theoretical basis for stabilizing messenger RNA through secondary structure design.Nucleic acids research · 2021Article
- Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus.Biophysical journal · 2021Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a theory of the dependence on sequence of the three-dimensional size of large single-stranded (ss) RNA molecules. The work is motivated by the fact that the genomes of many viruses are large ssRNA molecules-often several thousand nucleotides long-and that these RNAs are spontaneously packaged into small rigid protein shells. We argue that there has been evolutionary pressure for the genome to have overall spatial properties-including an appropriate radius of gyration, R(g)-that facilitate this assembly process. For an arbitrary RNA sequence, we introduce the (thermal) average maximum ladder distance (MLD) and use it as a measure of the "extendedness" of the RNA secondary structure. The MLD values of viral ssRNAs that package into capsids of fixed size are shown to be consistently smaller than those for randomly permuted sequences of the same length and base composition, and also smaller than those of natural ssRNAs that are not under evolutionary pressure to have a compact native form. By mapping these secondary structures onto a linear polymer model and by using MLD as a measure of effective contour length, we predict the R(g) values of viral ssRNAs are smaller than those of nonviral sequences. More generally, we predict the average MLD values of large nonviral ssRNAs scale as N(0.67+/-0.01), where N is the number of nucleotides, and that their R(g) values vary as MLD(0.5) in an ideal solvent, and hence as N(0.34). An alternative analysis, which explicitly includes all branches, is introduced and shown to yield consistent results.
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