ReviewJournal of molecular evolution2009
RNA-amino acid binding: a stereochemical era for the genetic code.
Review in Journal of molecular evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
97 citing papers in PubMed, 206 citations in OpenAlex.
- Genomic Codon Usage is Structurally Consistent with First-Classness Across the Tree of Life.Journal of molecular evolution · 2026Article
- RNA-binding protein transcripts reflect composition of target mRNAs.Nucleic acids research · 2026Article
- A framework for the exploration of subcellular compartmentalization of RNA-binding proteins.Nature communications · 2026Article
- Selection for growth drives the emergence of genetic heredity in protocells.PLoS biology · 2026Article
- Molecular Dissipative Structuring: The Fundamental Creative Force in Biology.Entropy (Basel, Switzerland) · 2026Review
- Avoiding Catastrophic Mutations Accurately Predicts Amino Acid to Codon Pairing.Journal of molecular evolution · 2026Article
- Is the emergence of life and of agency expected?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Structural Enzymology, Phylogenetics, Differentiation, and Symbolic Reflexivity at the Dawn of Biology.Genome biology and evolution · 2025Article
- Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tryptophan As a New Member of RNA-Induced Silencing Complexes Prevents Colon Cancer Liver Metastasis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Reflections on the Origin of Coded Protein Biosynthesis.Biomolecules · 2024Review
- An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA.Journal of the American Chemical Society · 2023Article
- The Non-Equilibrium Thermodynamics of Natural Selection: From Molecules to the Biosphere.Entropy (Basel, Switzerland) · 2023Article
- Mixed anhydrides at the intersection between peptide and RNA autocatalytic sets: evolution of biological coding.Interface focus · 2023Article
- Biophysical Interactions Underpin the Emergence of Information in the Genetic Code.Life (Basel, Switzerland) · 2023Article
- Screening for Primordial RNA-Peptide Interactions Using High-Density Peptide Arrays.Life (Basel, Switzerland) · 2023Article
- Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells.Life (Basel, Switzerland) · 2023Article
- A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism.Frontiers in microbiology · 2023Article
- Widespread autogenous mRNA-protein interactions detected by CLIP-seq.Nucleic acids research · 2022Article
- Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid-Phase and Template-Directed Chain Assembly.Chembiochem : a European journal of chemical biology · 2022Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
By combining crystallographic and NMR structural data for RNA-bound amino acids within riboswitches, aptamers, and RNPs, chemical principles governing specific RNA interaction with amino acids can be deduced. Such principles, which we summarize in a "polar profile", are useful in explaining newly selected specific RNA binding sites for free amino acids bearing varied side chains charged, neutral polar, aliphatic, and aromatic. Such amino acid sites can be queried for parallels to the genetic code. Using recent sequences for 337 independent binding sites directed to 8 amino acids and containing 18,551 nucleotides in all, we show a highly robust connection between amino acids and cognate coding triplets within their RNA binding sites. The apparent probability (P) that cognate triplets around these sites are unrelated to binding sites is congruent with 5.3 x 10(-45) for codons overall, and P congruent with 2.1 x 10(-46) for cognate anticodons. Therefore, some triplets are unequivocally localized near their present amino acids. Accordingly, there was likely a stereochemical era during evolution of the genetic code, relying on chemical interactions between amino acids and the tertiary structures of RNA binding sites. Use of cognate coding triplets in RNA binding sites is nevertheless sparse, with only 21% of possible triplets appearing. Reasoning from such broad recurrent trends in our results, a majority (approximately 75%) of modern amino acids entered the code in this stereochemical era; nevertheless, a minority (approximately 21%) of modern codons and anticodons were assigned via RNA binding sites. A Direct RNA Template scheme embodying a credible early history for coded peptide synthesis is readily constructed based on these observations.
Indexed as
Identifiers
What OpenQuestion holds
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.