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By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physicochemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of t RNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.","publication_date":"2008,,","publication_name":"Acta Biotheoretica","grobid_abstract_attachment_id":"65882871"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Evolution and RNA Relics. A Systems Biology View","broadcastable":true,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [16480167]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "full_page_mobile_sutd_modal"; window.loswp.useOptimizedScribd4genScript = false; window.loginModal = {}; window.loginModal.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":65882871,"attachmentType":"pdf"}"><img alt="First page of “Evolution and RNA Relics. A Systems Biology View”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/65882871/mini_magick20210304-31277-1k9z6kn.png?1614845077" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/images/single_work_splash/adobe_icon.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Evolution and RNA Relics. A Systems Biology View</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="16480167" href="https://ujf-grenoble.academia.edu/JDemongeot"><img alt="Profile image of Jacques Demongeot" class="ds-work-card--author-avatar" src="https://0.academia-photos.com/16480167/86887680/75559624/s65_jacques.demongeot.png" />Jacques Demongeot</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">2008, Acta Biotheoretica</p><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">21 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 45345741; const worksViewsPath = "/v0/works/views?subdomain_param=api&work_ids%5B%5D=45345741"; const getWorkViews = async (workId) => { const response = await fetch(worksViewsPath); if (!response.ok) { throw new Error('Failed to load work views'); } const data = await response.json(); return data.views[workId]; }; // Get the view count for the work - we send this immediately rather than waiting for // the DOM to load, so it can be available as soon as possible (but without holding up // the backend or other resource requests, because it's a bit expensive and not critical). const viewCount = await getWorkViews(workId); const updateViewCount = (viewCount) => { try { const viewCountNumber = parseInt(viewCount, 10); if (viewCountNumber === 0) { // Remove the whole views element if there are zero views. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); return; } const commaizedViewCount = viewCountNumber.toLocaleString(); const viewCountBody = document.getElementById('work-metadata-view-count'); if (!viewCountBody) { throw new Error('Failed to find work views element'); } viewCountBody.textContent = `${commaizedViewCount} views`; } catch (error) { // Remove the whole views element if there was some issue parsing. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); throw new Error(`Failed to parse view count: ${viewCount}`, error); } }; // If the DOM is still loading, wait for it to be ready before updating the view count. if (document.readyState === "loading") { document.addEventListener('DOMContentLoaded', () => { updateViewCount(viewCount); }); // Otherwise, just update it immediately. } else { updateViewCount(viewCount); } })();</script></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physicochemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of t RNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":65882871,"attachmentType":"pdf","workUrl":"https://www.academia.edu/45345741/Evolution_and_RNA_Relics_A_Systems_Biology_View"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":65882871,"attachmentType":"pdf","workUrl":"https://www.academia.edu/45345741/Evolution_and_RNA_Relics_A_Systems_Biology_View"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div></div><div data-auto_select="false" data-client_id="331998490334-rsn3chp12mbkiqhl6e7lu2q0mlbu0f1b" data-doc_id="65882871" data-landing_url="https://www.academia.edu/45345741/Evolution_and_RNA_Relics_A_Systems_Biology_View" data-login_uri="https://www.academia.edu/registrations/google_one_tap" data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="70386686" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/70386686/The_origin_of_the_genetic_code_amino_acids_as_cofactors_in_an_RNA_world">The origin of the genetic code: amino acids as cofactors in an RNA world</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="8579705" href="https://elte.academia.edu/EorsSzathmary">Eors Szathmary</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Trends in Genetics, 1999</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The origin of the genetic code: amino acids as cofactors in an RNA world","attachmentId":80162230,"attachmentType":"pdf","work_url":"https://www.academia.edu/70386686/The_origin_of_the_genetic_code_amino_acids_as_cofactors_in_an_RNA_world","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/70386686/The_origin_of_the_genetic_code_amino_acids_as_cofactors_in_an_RNA_world"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="36031480" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/36031480/Speculations_on_the_evolution_of_the_genetic_code_III_The_evolution_of_t_RNA">Speculations on the evolution of the genetic code III: The evolution of t-RNA</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="55487271" href="https://independent.academia.edu/HymanHartman1">Hyman Hartman</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Origins of Life and Evolution of Biospheres, 1984</p><p class="ds-related-work--abstract ds2-5-body-sm">It is postulated that the primitive genetic code was a doublet G, C code.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Speculations on the evolution of the genetic code III: The evolution of t-RNA","attachmentId":55917771,"attachmentType":"pdf","work_url":"https://www.academia.edu/36031480/Speculations_on_the_evolution_of_the_genetic_code_III_The_evolution_of_t_RNA","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/36031480/Speculations_on_the_evolution_of_the_genetic_code_III_The_evolution_of_t_RNA"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="12176972" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/12176972/Chemical_interactions_between_amino_acid_and_RNA_multiplicity_of_the_levels_of_specificity_explains_origin_of_the_genetic_code">Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30601357" href="https://otmed.academia.edu/HerveSeligmann">Herve Seligmann</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Die Naturwissenschaften, 2002</p><p class="ds-related-work--abstract ds2-5-body-sm">The emergence of the genetic code remains an enigma. Proposed mechanisms are based on random, historical, thermodynamic and natural selection. However, they introduce chance as a key factor for overcoming the difficulties encountered by the model. We propose here a model in which three successive levels of chemical specificity generated the nucleotide assignments of amino acids in the genetic code. The first level results from hydrophobic and stereospecific interactions between amino acids and short oligonucleotides (termed oligons). The second and third levels of specificity are determined by conditions of energy transfer from loaded oligons (amino acid-oligomer covalently linked) to formation of phosphodiester bond (second level of specificity) and peptidic bond (third level of specificity), while these reactions are catalyzed by RNA templates. This model is sustained by the relationships observed between dipole moments of the nucleotides (forming the anticodon) and reactivity of ...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code","attachmentId":37475878,"attachmentType":"pdf","work_url":"https://www.academia.edu/12176972/Chemical_interactions_between_amino_acid_and_RNA_multiplicity_of_the_levels_of_specificity_explains_origin_of_the_genetic_code","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/12176972/Chemical_interactions_between_amino_acid_and_RNA_multiplicity_of_the_levels_of_specificity_explains_origin_of_the_genetic_code"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="21514748" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/21514748/Physicochemical_Optimization_in_the_Genetic_Code_Origin_as_the_Number_of_Codified_Amino_Acids_Increases">Physicochemical Optimization in the Genetic Code Origin as the Number of Codified Amino Acids Increases</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="42610136" href="https://independent.academia.edu/MarioMedugno">Mario Medugno</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 1999</p><p class="ds-related-work--abstract ds2-5-body-sm">We have assumed that the coevolution theory of genetic code origin (Wong JT, Proc Natl Acad Sci USA 72:1909-1912) is essentially correct. This theory makes it possible to identify at least 10 evolutionary stages through which genetic code organization might have passed prior to reaching its current form. The calculation of the minimization level of all these evolutionary stages leads to the following conclusions. (1) The minimization percentages increased linearly with the number of amino acids codified in the codes of the various evolutionary stages when only the sense changes are considered in the analysis. This seems to favor the physicochemical theory of genetic code origin even if, as discussed in the paper, this observation is also compatible with the coevolution theory.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Physicochemical Optimization in the Genetic Code Origin as the Number of Codified Amino Acids Increases","attachmentId":41963026,"attachmentType":"pdf","work_url":"https://www.academia.edu/21514748/Physicochemical_Optimization_in_the_Genetic_Code_Origin_as_the_Number_of_Codified_Amino_Acids_Increases","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/21514748/Physicochemical_Optimization_in_the_Genetic_Code_Origin_as_the_Number_of_Codified_Amino_Acids_Increases"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="31020281" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/31020281/Barbieri_M_2015_Evolution_of_the_Genetic_Code_The_Ribosome_Oriented_Model">Barbieri M (2015) Evolution of the Genetic Code: The Ribosome-Oriented Model</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="214111" href="https://ferrara.academia.edu/MarcelloBarbieri">Marcello Barbieri</a></div><p class="ds-related-work--abstract ds2-5-body-sm">There are currently three major theories on the origin and evolution of the genetic code: the stereochem-ical theory, the coevolution theory, and the error-minimization theory. The first two assume that the genetic code originated respectively from chemical affinities and from metabolic relationships between codons and amino acids. The error-minimization theory maintains that in primitive systems the apparatus of protein synthesis was extremely prone to errors, and postulates that the genetic code evolved in order to minimize the deleterious effects of the translation errors. This article describes a fourth theory which starts from the hypothesis that the ancestral genetic code was ambiguous and proposes that its evolution took place with a mechanism that systematically reduced its ambiguity and eventually removed it altogether. This proposal is distinct from the stereochemical and the coevolu-tion theories because they do not contemplate any ambiguity in the genetic code, and it is distinct from the error-minimization theory because ambiguity-reduction is fundamentally different from error-minimization. The concept of ambiguity-reduction has been repeatedly mentioned in the scientific literature, but so far it has remained only an abstract possibility because no model has been proposed for its mechanism. Such a model is described in the present article and may be the first step in a new approach to the study of the evolution of the genetic code.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Barbieri M (2015) Evolution of the Genetic Code: The Ribosome-Oriented Model","attachmentId":51453100,"attachmentType":"pdf","work_url":"https://www.academia.edu/31020281/Barbieri_M_2015_Evolution_of_the_Genetic_Code_The_Ribosome_Oriented_Model","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/31020281/Barbieri_M_2015_Evolution_of_the_Genetic_Code_The_Ribosome_Oriented_Model"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="60744243" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/60744243/Evolution_of_the_genetic_code_the_nonsense_antisense_and_antinonsense_codes_make_no_sense">Evolution of the genetic code: the nonsense, antisense, and antinonsense codes make no sense</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="42188298" href="https://independent.academia.edu/GunnarHouen">Gunnar Houen</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Biosystems, 1999</p><p class="ds-related-work--abstract ds2-5-body-sm">According to the molecular recognition theory, the complementarity of the sense and nonsense DNA strands is reflected in a complementarity of polypeptides and the corresponding nonsense polypeptides. A comparison of the sense and nonsense code matrices, and of the antisense and antinonsense code matrices, either by visual inspection or by comparing the corresponding hydrophobicity matrices (e.g. by simply adding them together), revealed no complementarity of these pairs of matrices in terms of possible attractive physical forces. Instead, it was evident that the codes divide the amino acids into two major groups: hydrophilic and hydrophobic, a division which is directly correlated with the folding property of proteins. A simple primordial genetic code distinguishing between these two types of amino acids would have been capable of generating three-dimensionally folded peptides, which could stabilize coding RNAs by forming ribonucleoprotein complexes. This evolutionary scheme is reflected in the present organisation of information processing and storage in essentially all organisms. RNAs are processed and translated into proteins by ribonucleoproteins, while other steps in information retrieval and processing, such as DNA replication, transcription, protein folding and posttranslational processing, are catalyzed by proteins. This shows that the evolution of DNA as an information storage medium was a secondary event, unrelated to the evolution of the genetic code. From the primordial hydrophilic/hydrophobic (f.ex. Leu/Arg) code, evolution proceeded by introduction of a catalytic amino acid (Ser). The further evolution of the code has mainly served to increase the number of functional hydrophilic amino acids, since there has not been a great advantage in increasing the number of structural, hydrophobic amino acids. At some stage during the evolution of the genetic code, double-stranded DNA was introduced as a maximally safe genetic copy of RNA. This required the action of highly specific enzymes, and was therefore preceded by the refinement of the genetic code. As a conclusion of this evolutionary scheme, it can be inferred that, in general only the sense strand encodes proteins.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Evolution of the genetic code: the nonsense, antisense, and antinonsense codes make no sense","attachmentId":74049817,"attachmentType":"pdf","work_url":"https://www.academia.edu/60744243/Evolution_of_the_genetic_code_the_nonsense_antisense_and_antinonsense_codes_make_no_sense","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/60744243/Evolution_of_the_genetic_code_the_nonsense_antisense_and_antinonsense_codes_make_no_sense"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="58472550" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/58472550/Insuperable_Problems_Of_The_Genetic_Code_Initially_Emerging_In_An_RNA_World">Insuperable Problems Of The Genetic Code Initially Emerging In An RNA World</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="23452151" href="https://unc.academia.edu/CharlesCarter">Charles Carter</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide-RNA world.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Insuperable Problems Of The Genetic Code Initially Emerging In An RNA World","attachmentId":72866911,"attachmentType":"pdf","work_url":"https://www.academia.edu/58472550/Insuperable_Problems_Of_The_Genetic_Code_Initially_Emerging_In_An_RNA_World","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/58472550/Insuperable_Problems_Of_The_Genetic_Code_Initially_Emerging_In_An_RNA_World"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="32676062" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/32676062/RNA_Amino_Acid_Binding_A_Stereochemical_Era_for_the_Genetic_Code">RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="63566792" href="https://colorado.academia.edu/MichaelYarus">Michael Yarus</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="63547820" href="https://independent.academia.edu/JeremyWidmann">Jeremy Widmann</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 2009</p><p class="ds-related-work--abstract ds2-5-body-sm">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 %5.3 9 10 -45 for codons overall, and P % 2.1 9 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.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code","attachmentId":52842441,"attachmentType":"pdf","work_url":"https://www.academia.edu/32676062/RNA_Amino_Acid_Binding_A_Stereochemical_Era_for_the_Genetic_Code","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/32676062/RNA_Amino_Acid_Binding_A_Stereochemical_Era_for_the_Genetic_Code"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="45515508" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/45515508/Acta_Biotheoretica_Mathematical_and_philosophical_foundations_of_biological_and_biomedical_science_The_Uroboros_Theory_of_Lifes_Origin_22_Nucleotide_Theoretical_Minimal_RNA_Rings_Reflect_Evolution_of_Genetic_Code_and_tRNA_rRNA_Translation_Machineries">Acta Biotheoretica Mathematical and philosophical foundations of biological and biomedical science The Uroboros Theory of Life's Origin: 22- Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30601357" href="https://otmed.academia.edu/HerveSeligmann">Herve Seligmann</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Your article is protected by copyright and all rights are held exclusively by Springer Nature B.V.. This e-offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com".</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Acta Biotheoretica Mathematical and philosophical foundations of biological and biomedical science The Uroboros Theory of Life's Origin: 22- Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries","attachmentId":66004573,"attachmentType":"pdf","work_url":"https://www.academia.edu/45515508/Acta_Biotheoretica_Mathematical_and_philosophical_foundations_of_biological_and_biomedical_science_The_Uroboros_Theory_of_Lifes_Origin_22_Nucleotide_Theoretical_Minimal_RNA_Rings_Reflect_Evolution_of_Genetic_Code_and_tRNA_rRNA_Translation_Machineries","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/45515508/Acta_Biotheoretica_Mathematical_and_philosophical_foundations_of_biological_and_biomedical_science_The_Uroboros_Theory_of_Lifes_Origin_22_Nucleotide_Theoretical_Minimal_RNA_Rings_Reflect_Evolution_of_Genetic_Code_and_tRNA_rRNA_Translation_Machineries"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="21514747" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/21514747/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code">The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="42610136" href="https://independent.academia.edu/MarioMedugno">Mario Medugno</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Molecular Evolution, 1998</p><p class="ds-related-work--abstract ds2-5-body-sm">Two forces are in general, hypothesized to have influenced the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships. In view of this, we have considered a model incorporating these two forces. In particular, we have studied the optimization level of the physicochemical properties of amino acids in the set of amino acid permutation codes that respects the biosynthetic relationships between amino acids. Where the properties of amino acids are represented by polarity and molecular volume we obtain indetermination percentages in the organization of the genetic code of approximately 40%. This indicates that the contingent factor played a significant role in structuring the genetic code. Furthermore, this result is in agreement with the genetic code coevolution hypothesis, which attributes a merely ancillary role to the properties of amino acids while it suggests that it was their biosynthetic relationships that organized the code. Furthermore, this result does not favor the stereochemical models proposed to explain the origin of the genetic code. On the other hand, where the properties of amino acids are represented by polarity alone, we obtain an indetermination percentage of at least 21.5%. This might suggest that the polarity distances played an important role and would therefore provide evidence in favor of the physicochemical hypothesis of genetic code origin. Although, overall, the analysis might have given stronger support to the latter hypothesis, this did not actually occur. The results are therefore discussed in the context of the different theories proposed to explain the origin of the genetic code.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code","attachmentId":41963028,"attachmentType":"pdf","work_url":"https://www.academia.edu/21514747/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/21514747/The_Historical_Factor_The_Biosynthetic_Relationships_Between_Amino_Acids_and_Their_Physicochemical_Properties_in_the_Origin_of_the_Genetic_Code"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":65882871,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":65882871,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_65882871" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="24912488" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/24912488/Degeneracy_in_the_Genetic_Code_How_and_Why">Degeneracy in the Genetic Code: How and Why?</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="46886295" href="https://independent.academia.edu/GlobalScienceBooks">Global Science Books</a></div><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Degeneracy in the Genetic Code: How and Why?","attachmentId":45239905,"attachmentType":"pdf","work_url":"https://www.academia.edu/24912488/Degeneracy_in_the_Genetic_Code_How_and_Why","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/24912488/Degeneracy_in_the_Genetic_Code_How_and_Why"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="1" data-entity-id="115960029" data-sort-order="default"><a class="ds-related-work--title 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code","attachmentId":112222789,"attachmentType":"pdf","work_url":"https://www.academia.edu/115960029/Some_aspects_of_the_organization_and_evolution_of_the_genetic_code","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/115960029/Some_aspects_of_the_organization_and_evolution_of_the_genetic_code"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="2" data-entity-id="6996930" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" 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