ArticleRNA (New York, N.Y.)2003
Finding specific RNA motifs: function in a zeptomole world?
Article in RNA (New York, N.Y.), 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 58 citations in OpenAlex.
- Assembly of catalytic complexes from randomized oligonucleotides.Science advances · 2025Article
- Pushing the Limits of Nucleic Acid Function.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Single-round deoxyribozyme discovery.Nucleic acids research · 2021Article
- The Genetic Code and RNA-Amino Acid Affinities.Life (Basel, Switzerland) · 2017Review
- The Optimization and Characterization of an RNA-Cleaving Fluorogenic DNAzyme Probe for MDA-MB-231 Cell Detection.Sensors (Basel, Switzerland) · 2017Article
- Improving the odds: Influence of starting pools on in vitro selection outcomes.Methods (San Diego, Calif.) · 2016Review
- Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach.Computational and structural biotechnology journal · 2014Review
- Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.Nucleic acids research · 2012Article
- Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.RNA (New York, N.Y.) · 2010Article
- A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype.Nucleic acids research · 2009Article
- The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers.RNA (New York, N.Y.) · 2009Article
- Rapid and simple ribozymic aminoacylation using three conserved nucleotides.Journal of the American Chemical Society · 2009Article
- Man versus machine versus ribozyme.PLoS biology · 2008Article
- Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme.Nucleic acids research · 2008Article
- Multiple pattern matching: a Markov chain approach.Journal of mathematical biology · 2008Article
- Question 5: on the chemical reality of the RNA world.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2007Article
- Functional information and the emergence of biocomplexity.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- RNA aptamers directed to discrete functional sites on a single protein structural domain.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Modular evolution and increase of functional complexity in replicating RNA molecules.RNA (New York, N.Y.) · 2007Article
- The building blocks and motifs of RNA architecture.Current opinion in structural biology · 2006Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Registered trials
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