ArticleHeliyon2017
Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias.
Article in Heliyon, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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.
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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.
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Who cites it
7 citing papers in PubMed, 8 citations in OpenAlex.
- The CpG Landscape of Protein Coding DNA in Vertebrates.Evolutionary applications · 2025Article
- Low Complexity Regions in Proteins and DNA are Poorly Correlated.Molecular biology and evolution · 2023Article
- A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences.BMC genomics · 2021Article
- A report on DNA sequence determinants in gene expression.Bioinformation · 2020Article
- Article
- Polyglutamine Repeats in Viruses.Molecular neurobiology · 2019Review
- Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length.Genome biology and evolution · 2018Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes.
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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.