An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences
Purine bias, which is usually referred to as an “ancestral codon”, is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the produ...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2015-01-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.4137/BBI.S24021 |
| _version_ | 1819037435934277632 |
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| author | Nicolas Carels Miguel Ponce de Leon |
| author_facet | Nicolas Carels Miguel Ponce de Leon |
| author_sort | Nicolas Carels |
| collection | DOAJ |
| description | Purine bias, which is usually referred to as an “ancestral codon”, is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller's spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins. |
| first_indexed | 2024-12-21T08:21:23Z |
| format | Article |
| id | doaj.art-4777d684a96b45a3bf9cd053c6fb753a |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-12-21T08:21:23Z |
| publishDate | 2015-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-4777d684a96b45a3bf9cd053c6fb753a2022-12-21T19:10:26ZengSAGE PublishingBioinformatics and Biology Insights1177-93222015-01-01910.4137/BBI.S24021An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding SequencesNicolas Carels0Miguel Ponce de Leon1Laboratório de Modelagem de Sistemas Biológicos, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT/IDN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil.Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid, Spain.Purine bias, which is usually referred to as an “ancestral codon”, is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller's spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins.https://doi.org/10.4137/BBI.S24021 |
| spellingShingle | Nicolas Carels Miguel Ponce de Leon An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences Bioinformatics and Biology Insights |
| title | An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences |
| title_full | An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences |
| title_fullStr | An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences |
| title_full_unstemmed | An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences |
| title_short | An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences |
| title_sort | interpretation of the ancestral codon from miller s amino acids and nucleotide correlations in modern coding sequences |
| url | https://doi.org/10.4137/BBI.S24021 |
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