Arithmetic inside the universal genetic code

BioSystems

Volumn 70, Issue 3, 2003, Pages 187-209

  ShCherbak, Vladimir I ^a  

^a AL FARABI KAZAKH NATIONAL UNIVERSITY   (Kazakhstan)

Author keywords

Arithmetic power; Genetic code; Genetic language; Mathematical model; Natural biocomputer

Indexed keywords

AMINO ACID; NUCLEIC ACID BASE;

GENETICS; MATHEMATICS;

ARITHMETIC; COMPUTER SYSTEM; CORRELATION ANALYSIS; ESCHERICHIA COLI; EUPLOTES; GENETIC ANALYSIS; GENETIC CODE; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; NONHUMAN; REVIEW; THEORETICAL MODEL;

ESCHERICHIA COLI; EUPLOTES; EUPLOTES OCTOCARINATUS;

EID: 0042662957     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(03)00066-2     Document Type: Article

References (57)

1. Adleman L.M. Molecular computation of solutions to combinatorial problems. Science. 266:1994;1021-1023.
2. Bertman M.O., Jungck J.R. Group graph of the genetic code. J. Heredity. 70:1979;379-384.
3. Crick F.H.C. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19:1966;548-555.
4. Crick F.H.C. The origin of the genetic code. J. Mol. Biol. 38:1968;367-379.
5. Crick F.H.C., Brenner S., Klug A., Pieczenik G. A speculation on the origin of protein synthesis. Origins Life. 7:1976;389-397.
6. Chen J., Wood D.H. Computation with biomolecules. Proc. Natl. Acad. Sci. U.S.A. 97:2000;1328-1330.
7. Dankwerts H.J., Neubert D. Symmetries of the genetic code doublets. J. Mol. Evol. 5:1975;327-332.
8. Eigen, M., Winkler, R., 1985. Das Spiel. Piper Verlag, München, Zürich, pp. 281-316.
9. Faulhammer D., Cukras A.R., Lipton R.J., Landweber L.F. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. U.S.A. 97:2000;1385-1389.
10. Figureau A. Information theory and the genetic code. Origins Life. 17:1987;439-449.
11. Freeland S.J., Hurst L.D. The genetic code is one in a million. J. Mol. Evol. 47:1998;238-248.
12. Gamow G. Possible relation between deoxyribonucleic acid and protein structures. Nature. 13:1954;318.
13. Goldberg A.L., Wittes R.E. Genetic code: aspects of organization. Science. 153:1966;420-424.
14. Greenstein, J.P., Winitz, M., 1991. Chemistry of the Amino Acids. John Wiley and Sons, Inc., New York, London.
15. Cys with GCA anticodon encoded on a single macromolecular DNA molecule. Nucleic Acids Res. 26:1998;4557-4565.
16. Hasegawa M., Miyata T. On the antisymmetry of the amino acid code table. Origins Life. 10:1980;265-270.
17. Jiménez-Montaño M.A. On the syntactic structure and redundancy distribution of the genetic code. BioSystems. 32:1993;11-23.
18. Jiménez-Montaño M.A. Protein evolution drives the evolution of the genetic code and vice versa. BioSystems. 54:1999;47-64.
19. Jiménez-Montaño M.A., de la Mora-Basañez C.R., Poeschel T. The hypercube structure of the genetic code explains conservative and non-conservative amino acid substitutions in vivo and in vitro. BioSystems. 39:1996;379-384.
20. Jukes T.H. Evolution of the amino acid code: inferences from mitochondrial codes. J. Mol. Evol. 19:1983;219-225.
21. Jukes T.H., Osawa S. The genetic code in mitochondria and chloroplasts. Experimentia. 46:1990;1117-1126.
22. Jungck J.R. The genetic code as periodic table. J. Mol. Evol. 11:1978;211-224.
23. Karasev V.A., Sorokin S.G. Topological structure of the genetic code. Russian J. Genetics. 33:1997;622-628.
24. Kashkarov, V.V., Krassovitskiy, A.M., Mamleev, V.S., shCherbak, V.I., 2002. Random sequences of proteins are exactly balanced like the canonical base pairs of DNA. In: Proceedings of the 10th ISSOL Meeting and 13th International Conference on the Origin of Life, Oaxaca City, Mexico, June 30-July 4.
25. Knight R.D., Freeland S.J., Landweber L.F. Selection, history and chemistry: the three faces of the genetic code. Trends Biochem. Sci. 24:1999;241-247.
26. Konopelchenko B.G., Rumer Yu.B. The codon classification inside genetic code. Docl. Acad. Nauk. SSSR. 223:1975;471-474.
27. Lacey J.C. Jr., Mullins D.W. Jr. Experimental studies related to the origin of the genetic code and the process of protein synthesis - a review. Origins Life. 13:1983;3-42.
28. Landweber L.F., Gilbert W. RNA editing as a source of genetic variation. Nature. 363:1993;179-182.
29. Landweber L.F., Kuo T.-C., Curtis E. Evolution and assembly of an extremely scrambled gene. Proc. Natl. Acad. Sci. U.S.A. 97:2000;3298-3303.
30. Lehman N., Jukes T.H. The genetic code development by stop codon takeover. J. Theor. Biol. 135:1988;203-214.
31. Lewin, B., 1987. Genes. John Wiley and Sons, Inc., New York, London.
32. Mac Dynaill D.A. A parity code interpretation of nucleotide alphabet composition. Chem. Commun. 18:2002;2062-2063.
33. Marshal R.E., Cascey T.C., Nirenberg M. Fine structure of RNA codewords recognized by bacterial, amphibian and mammalian transfer RNA. Science. 155:1967;820-825.
34. Meyer F., Schmidt H.I., Plümper E., Hasilik A., Mersmann G., Meyer H.E., Engström A., Heckmann K. UGA is translated as cysteine in pheromone 3 of Euplotes octocarinatus. Proc. Natl. Acad. Sci. U.S.A. 88:1991;3758-3761.
35. Porschke D. Differential effect of amino acid residues on the stability of double helices formed from polyribonucleotides and its possible relation to the evolution of the genetic code. J. Mol. Evol. 21:1985;192-198.
36. Rosen G. Molecular content relations in the genetic code. Phys. Lett. A. 253:1999;354-357.
37. Rumer Yu.B. About systematization of the codons of the genetic code. Dokl. Acad. Nauk. SSSR. 167:1966;1393-1394.
38. Shcherbak V.I. The co-operative symmetry of the genetic code. J. Theor. Biol. 132:1988;121-124.
39. Shcherbak V.I. Rumer's rule and transformation in the context of the co-operative symmetry of the genetic code. J. Theor. Biol. 139:1989a;271-276.
40. Shcherbak V.I. Ways of wobble pairing are formalized with the co-operative symmetry of the genetic code. J. Theor. Biol. 139:1989b;277-281.
41. Shcherbak V.I. The "START" and "STOP" of the genetic code: why exactly ATG and TAG, TAA? J. Theor. Biol. 139:1989c;283-286.
42. Shcherbak V.I. The symmetrical architecture of the genetic code systematization principle. J. Theor. Biol. 162:1993a;395-398.
43. Shcherbak V.I. Twenty canonical amino acids of the genetic code: the arithmetical regularities. Part I. J. Theor. Biol. 162:1993b;399-401.
44. Shcherbak V.I. Sixty-four triplets and 20 canonical amino acids of the genetic code: the arithmetical regularities. Part II. J. Theor. Biol. 166:1994;475-477.
45. Shcherbak, V.I., 1996. A new manifestation of the arithmetical regularity suggests the universal genetic code distinguishes the decimal system. In: Proceedings of the 11th International Conference Origin of Life, Book of Abstracts, Orleans July 5-12, France.
46. Shcherbak, V.I., 1999. A new manifestation of the decimal system in the genetic code. In: Proceedings of the 12th International Conference Origin of Life, Book of Abstracts, San-Diego, July 11-16, USA.
47. Shulz, G.E., Schirmer, R.H., 1979. Principles of Protein Structure. Springer-Verlag, New York, Heidelberg, Berlin.
48. Siemion I.Z. Compositional frequencies of amino acids in the proteins and the genetic code. BioSystems. 32:1994;163-170.
49. Sjöström M., Wold S. A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids. J. Mol. Evol. 22:1985;272-277.
50. Sukhodolets V.V. The genetic code as a clue of molecular evolution. J. Theor. Biol. 141:1989;379-389.
51. Tan M., Heckmann K. The two γ-tubulin-encoding genes of the ciliate Euplotes crassus differ in their sequences, codon usage, transcription initiation sites and poly(A) addition sites. Gene. 210:1998;53-60.
52. Tan M., Heckmann K., Brünen-Nieweler C. The micronuclear gene encoding a putative aminoacyl-tRNA synthetase cofactor of the ciliate Euplotes octocarinatus is interrupted by two sequences that are removed during macromolecular development. Gene. 233:1999;131-140.
53. Verkhovod A.B. Alphanumerical division of the universal genetic code: new divisions reveal new balances. J. Theor. Biol. 170:1994;327-330.
54. Volkenstein M.V. The genetic code of protein structures. Biochim. Biophys. Acta. 119:1966;421-424.
55. Yockey, H.P., 1992. Information Theory and Molecular Biology. Cambridge University Press, Cambridge, New York.
56. Yockey H.P. Origin of life on earth and Shannon's theory of communication. Comput. Chem. 24:2000;105-123.
57. Zhang C.T. A symmetrical theory of DNA sequences and its applications. J. Theor. Biol. 187:1997;297-306.