p-Adic Modelling of the Genome and the Genetic Code

This paper presents the foundations of p-adic modelling in genomics. Considering nucleotides, codons, DNA and RNA sequences, amino acids and proteins as information systems, we have formulated the corresponding p-adic formalisms for their investigations. Each of these systems has its characteristic prime number used for construction of the related information space. Relevance of this approach is illustrated by some examples. In particular, it is shown that degeneration of the genetic code is a p-adic phenomenon. We have also put a forward a hypothesis on the evolution of the genetic code assuming that primitive code was based on single nucleotides and chronologically first four amino acids. This formalism of p-adic genomic information systems can be implemented in computer programs and applied to various concrete cases.

[1]  A. Khrennikov.  Information Dynamics in Cognitive, Psychological, Social, and Anomalous Phenomena , 2004 .

[2]  S. V. Kozyrev,et al.  Genetic code on the diadic plane , 2007, q-bio/0701007.

[3]  V I L F M Y W P G D N S A C E H K Q R T,et al.  Amino Acid , 2020, Definitions.

[4]  Peter D. Jarvis,et al.  Codon and nucleotide assignments in a supersymmetric model of the genetic code , 1997 .

[5]  Andrei Khrennikov,et al.  Gene expression from polynomial dynamics in the 2-adic information space , 2006, q-bio/0611068.

[6]  P. Freund,et al.  p-adic numbers in physics , 1993 .

[7]  Branko Dragovich,et al.  p-Adic Degeneracy of the Genetic Code , 2007, ArXiv.

[8]  Siegfried Bosch,et al.  p-adic Analysis , 1990 .

[9]  R. Swanson.  A unifying concept for the amino acid code. , 1984, Bulletin of mathematical biology.

[10]  V A Avetisov,et al.  p-adic models of ultrametric diffusion constrained by hierarchical energy landscapes , 2002 .

[11]  Branko Dragovich,et al.  p-Adic and Adelic Quantum Mechanics , 2003, hep-th/0312046.

[12]  B. Dragovich.  p‐Adic and Adelic Cosmology: p‐Adic Origin of Dark Energy and Dark Matter , 2006, hep-th/0602044.

[13]  Hornos.  Algebraic model for the evolution of the genetic code. , 1993, Physical review letters.

[14]  C. Q. Lee,et al.  The Computer Journal , 1958, Nature.

[15]  Iu B Rumer.  [Systematization of codons in the genetic code]. , 1968, Doklady Akademii nauk SSSR.

[16]  L. Frappat,et al.  Crystalizing the Genetic Code , 2000, Journal of biological physics.

[17]  Edward N. Trifonov,et al.  The Triplet Code From First Principles , 2004, Journal of biomolecular structure & dynamics.

[18]  Fernando Q. Gouvêa,et al.  P-Adic Numbers: An Introduction , 1993 .

[19]  Laura F. Landweber,et al.  Rewiring the keyboard: evolvability of the genetic code , 2001, Nature Reviews Genetics.

[20]  T. Jukes.  Evolution of the amino acid code: Inferences from mitochondrial codes , 2005, Journal of Molecular Evolution.

[21]  M. Forger,et al.  Lie superalgebras and the multiplet structure of the genetic code. I. Codon representations , 2000 .

[22]  S. V. Kozyrev,et al.  On p-adic mathematical physics , 2006, 0904.4205.

[23]  S. Osawa,et al.  Recent evidence for evolution of the genetic code , 1992, Microbiological reviews.

[24]  J. Wong.  A co-evolution theory of the genetic code. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Jayanth R Banavar,et al.  Physics of proteins. , 2007, Annual review of biophysics and biomolecular structure.

[26]  Brian Hayes,et al.  THE INVENTION OF THE GENETIC CODE , 1998 .

[27]  F. H. C. CRICK,et al.  Origin of the Genetic Code , 1967, Nature.

[28]  Grace Jordison.  Molecular Biology of the Gene , 1965, The Yale Journal of Biology and Medicine.

[29]  Rumer IuB.  Systematization of codons in the genetic code , 1969 .

[30]  V. S. Vladimirov,et al.  P-adic analysis and mathematical physics , 1994 .

[31]  Branko Dragovich,et al.  A p-adic model of DNA sequence and genetic code , 2006, ArXiv.