Finding specific RNA motifs: function in a zeptomole world?
Open accessAbstract
We have developed a new method for estimating the abundance of any modular (piecewise) RNA motif within a longer random region. We have used this method to estimate the size of the active motifs available to modern SELEX experiments (picomoles of unique sequences) and to a plausible RNA World (zeptomoles of unique sequences: 1 zmole = 602 sequences). Unexpectedly, activities such as specific isoleucine binding are almost certainly present in zeptomoles of molecules, and even ribozymes such as self-cleavage motifs may appear (depending on assumptions about the minimal structures). The number of specified nucleotides is not the only important determinant of a motif’s rarity: The number of modules into which it is divided, and the details of this division, are also crucial. We propose three maxims for easily isolated motifs: the Maxim of Minimization, the Maxim of Multiplicity, and the Maxim of the Median. These maxims together state that selected motifs should be small and composed of as many separate, equally sized modules as possible. For evenly divided motifs with four modules, the largest accessible activity in picomole scale (1–1000 pmole) pools of length 100 is about 34 nucleotides; while for zeptomole scale (1–1000 zmole) pools it is about 20 specific nucleotides (50% probability of occurrence). This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules.
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Template-directed ligation would shift the pool toward longer sequences.
“In addition, our simulations indicate that template-directed ligation would shift the pool toward longer sequences, another important factor for activity (31,32).”
From Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences (2012) · cites this paper as [31]
Functions that can be performed by short motifs, such as aminoacylation or self-cleavage, could potentially be found even in highly biased sequence pools since the probability of finding the motif is relatively large.
“Functions that can be performed by short motifs, such as aminoacylation or self-cleavage (24,31,74), could potentially be found even in highly biased sequence pools since the probability of finding the motif is relatively large.”
From Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences (2012) · cites this paper as [31]
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- Authors
- KNIGHT, R., & YARUS, M.
- Affiliations
- University of Colorado Boulder (US)
- Corresponding author
- YARUS, MICHAEL
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2003-02
- Volume
- 9
- Issue
- 2
- Pages
- 218-230
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC1370388
- OpenAlex
- W2107321275
- Cited by
- 58
- References
- 21
- Citations by year
- 2025: 1 · 2024: 3 · 2022: 1 · 2021: 1 · 2020: 2 · 2019: 2 · 2017: 2 · 2016: 2 · 2014: 1 · 2012: 3
- FWCI
- 2.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- SELEX, RNA world, ribozymes, aptamers
- MeSH terms
- Animals, Computer Simulation, Humans, Models, Genetic, RNA, RNA, Catalytic, Sequence Analysis, RNA
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