On the codon evolution (original) (raw)
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Crystal basis model: Codon-Anticodon interaction and genetic code evolution
P-Adic Numbers, Ultrametric Analysis, and Applications
Imposing a minimum principle in the framework of the so called crystal basis model of the genetic code, we determine the structure of the minimum set of 22 anticodons which allows the translational-transcription for animal mitochondrial code. The results are in very good agreement with the observed anticodons. Then, we analyze the evolution of the genetic code, with 20 amino acids encoded from the beginning, from the viewpoint of codon-anticodon interaction. Following the same spirit as above, we determine the structure of the anticodons in the Ancient, Archetypal and Early Genetic codes. Most of our results agree with the generally accepted scheme.
Pure and Applied Chemistry, 1993
The universal correspondence between the primary structure of a gene, characterized by a unique sequence of only four different nucleotide residues, and the primary structure of a protein, characterized by a given sequence of twenty different amino acid residues, is known as the "genetic code". This code is degenerated in the sense that a group of six, four or just two synonymous codons can code for a given amino acid. In this paper I will discuss only the special features of duet codons and in particular the effect of the purine/pyrimidine base proper in the third position, the observed substitution frequency, and the major determinant of the codon usage bias in prokaryots and in eukaryots.
Nucleic Acids Research, 1980
In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, U'acil Guanine and Cytosine have been reported. Non bonded induce& polarization and dispersion potentials are not taken into account. Ilectrostatic hard sphere model of Nash and Bradley has been employed. Computations have been performed to find out the minimum energy configuration out of the various possible com lex configurations. Results have been discussed with referenceto similar calculations with G-C base pair performed by the authors.
Combinatorics, Homology and Symmetry of codons
In nuclear physics and elementary particle theory concept of unitary symmetry and the related idea of the hierarchy of interactions play a fundamental role [1, 2]. So the relative smallness of the electromagnetic and weak interactions as compared to the strong interaction of the nucleons in the nucleus can be considered a model of the nucleus in the limit of exact symmetry of the strong interactions. In this model, protons and neutrons are physically indistinguishable states of the nucleon, and the properties of the nucleus are invariant under isotopic transformations. In the case of molecules, we can also talk about the hierarchy of interactions involved in their formation. As an example of a "strong" interaction here we can point to energy of chemical bonds, which is 1-2 orders of magnitude more energy non-bonded interactions. Another example - when the energy of valence interactions is much greater than the energy of intermolecular bonds in the condensed medium. Usually accounting of weak interactions in 'chemistry is performed by introducing a physical model of various perturbations. These perturbations typically are unmeasured parameters that; are essentially the fitting values. However, in the preferred class of molecules can try to find such values of the parameter in the ratio in which the contributions of the "weak" interactions are compensated or negligible. Symmetry approach is important in estimation of reliability of experimental data and to predict new values of a parameter. The same, from the standpoint of finding a unitary symmetry, the approach would be interesting to extend to more complex molecules and molecular systems. Up until genetic. The application of the previously developed concepts of symmetry to the codon is the purpose of this work. Keywords: Codons, Combinatory, Homology, Homologous series, Unitary Symmetry.
Journal of Molecular Modeling, 2012
Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the Hbonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.
Unitary symmetry of codons. The keystone laws of mutagenesis and evolution
Chemical objects are ideal for field testing of combinatorial representations and their physical applications. These objects are countable discrete structures. Combinations of the proton and neutron with repetitions are all nuclear system. Combinations of nuclei and electrons with repetitions represent the whole system of chemical elements and their ions. Combinations of atoms with repetitions and permutations give rise to a huge number of molecules. All these countable discrete structures and would remain interesting amusements if not the manifestation in a set of combinations the features of homology. But are not generally accepted notions about " accession homology ", and notions of " substitution homology ". But even the idea of "substitution homology " would remain important, but not the need to clarify in theory of homologous series if we had not introduced "substitution homology" as a set of two-link transitions. It turned out that the two-link transitions between homologues in the space of their physical and chemical parameters are arranged regularly. So regularly, we can talk about the manifestation of the invariance of the two-link homology location, i.e. the existence of a special symmetry, unitary symmetry. The theoretical aspects of unitary symmetry of nuclear, atoms and molecules presents in many of my articles [1,2,3,4,5]. The experimental confirmation of its existence presents in [6,7]. This article will consider the necessary and sufficient conditions for the the consideration of the genetic code within Paradigm "the original discrete elements - a combination of discrete components - screening of combinatorial objects within real Homeostasis - the construction of two-link homology system - selection of two-link homologies in all possible replacements of initial discrete elements - finding of invariant of two-link homologies.
When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to 'evolve' from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven 'molecular Darwinism'. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales. 'Evolving' all codons from each other through sequential series of transitions and transversions 4 Correlating trimeric duplex stability with amino acid coding properties 5 Correlations between larger domain DNA energy profiles and higher-order biological functions 6 Concluding remarks 6 Going forward 7
An integrated, structure- and energy-based view of the genetic code
Nucleic acids research, 2016
The principles of mRNA decoding are conserved among all extant life forms. We present an integrative view of all the interaction networks between mRNA, tRNA and rRNA: the intrinsic stability of codon-anticodon duplex, the conformation of the anticodon hairpin, the presence of modified nucleotides, the occurrence of non-Watson-Crick pairs in the codon-anticodon helix and the interactions with bases of rRNA at the A-site decoding site. We derive a more information-rich, alternative representation of the genetic code, that is circular with an unsymmetrical distribution of codons leading to a clear segregation between GC-rich 4-codon boxes and AU-rich 2:2-codon and 3:1-codon boxes. All tRNA sequence variations can be visualized, within an internal structural and energy framework, for each organism, and each anticodon of the sense codons. The multiplicity and complexity of nucleotide modifications at positions 34 and 37 of the anticodon loop segregate meaningfully, and correlate well wit...
Dependence of nucleotide physical properties on their placement in codons and determinative degree
Journal of Zhejiang University Science, 2005
Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (Austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependences of these variables from the place in the codon and the determinative degree were obtained. The difference of these variables for codons and anticodons is shown.