An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences

An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences

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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...

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Main Authors: Nicolas Carels, Miguel Ponce de Leon
Format: Article
Language:English
Published: SAGE Publishing 2015-01-01
Series:Bioinformatics and Biology Insights
Online Access:https://doi.org/10.4137/BBI.S24021
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spelling doaj-4777d684a96b45a3bf9cd053c6fb753a2020-11-25T02:34:09ZengSAGE 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
collection DOAJ
language English
format Article
sources DOAJ
author Nicolas Carels
Miguel Ponce de Leon
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
author_facet Nicolas Carels
Miguel Ponce de Leon
author_sort Nicolas Carels
title 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_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_sort interpretation of the ancestral codon from miller's amino acids and nucleotide correlations in modern coding sequences
publisher SAGE Publishing
series Bioinformatics and Biology Insights
issn 1177-9322
publishDate 2015-01-01
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.
url https://doi.org/10.4137/BBI.S24021
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