Full Text:   <1661>

CLC number: Q34

On-line Access: 

Received: 2005-04-26

Revision Accepted: 2005-05-30

Crosschecked: 0000-00-00

Cited: 3

Clicked: 3354

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE B 2005 Vol.6 No.8 P.743~755

http://doi.org/10.1631/jzus.2005.B0743


DNA sequence representation by trianders and determinative degree of nucleotides


Author(s):  DUPLIJ Diana, DUPLIJ Steven

Affiliation(s):  Institute of Molecular Biology and Genetics, Kiev 03143, Ukraine; more

Corresponding email(s):   Steven.A.Duplij@univer.kharkov.ua

Key Words:  DNA walk, Triander, Determinative degree, Analysis DNA sequences, Dystrophin, Nucleotide


DUPLIJ Diana, DUPLIJ Steven. DNA sequence representation by trianders and determinative degree of nucleotides[J]. Journal of Zhejiang University Science B, 2005, 6(8): 743~755.

@article{title="DNA sequence representation by trianders and determinative degree of nucleotides",
author="DUPLIJ Diana, DUPLIJ Steven",
journal="Journal of Zhejiang University Science B",
volume="6",
number="8",
pages="743~755",
year="2005",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2005.B0743"
}

%0 Journal Article
%T DNA sequence representation by trianders and determinative degree of nucleotides
%A DUPLIJ Diana
%A DUPLIJ Steven
%J Journal of Zhejiang University SCIENCE B
%V 6
%N 8
%P 743~755
%@ 1673-1581
%D 2005
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2005.B0743

TY - JOUR
T1 - DNA sequence representation by trianders and determinative degree of nucleotides
A1 - DUPLIJ Diana
A1 - DUPLIJ Steven
J0 - Journal of Zhejiang University Science B
VL - 6
IS - 8
SP - 743
EP - 755
%@ 1673-1581
Y1 - 2005
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2005.B0743


Abstract: 
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the “fine structure” of nucleotide sequences. The approach is based on the assumption that nucleotides have an inner abstract characteristic, the determinative degree, which reflects genetic code phenomenological properties and is adjusted to nucleotides physical properties. We consider each codon position independently, which gives three separate walks characterized by different angles and lengths, and that such an object is called triander which reflects the “strength” of branch. A general method for identifying DNA sequence “by triander” which can be treated as a unique “genogram” (or “gene passport”) is proposed. The two- and three-dimensional trianders are considered. The difference of sequences fine structure in genes and the intergenic space is shown. A clear triplet signal in coding sequences was found which is absent in the intergenic space and is independent from the sequence length. This paper presents the topological classification of trianders which can allow us to provide a detailed working out signatures of functionally different genomic regions.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1] Arnold, V.I., Oleinik, O.A., 1979. Topology of real algebraic manifolds. Vestnik Mosk. Univ. Ser. I Mat. I Mekh., A249:7-17.

[2] Azbel, M.Y., 1973. Random two-component one-dimensional Ising model for heteropolymer melting. Phys. Rev. Lett., 31:589-592.

[3] Azbel, M.Y., 1995. Universality of DNA statistical structure. Phys. Rev. Lett., 75:168-171.

[4] Bashford, J.D., Tsohantjis, I., Jarvis, P.D., 1997. Codon and nucleotide assignments in a supersymmetric model of the genetic code. Phys. Lett., A233:481-488.

[5] Bergmann, S., Ihmels, J., Barkai, N., 2002. Self-similarity Limits of Genomic Signatures. Weizmann Inst. Science Preprint, Cond-mat/0210038, Rehovot, p.12.

[6] Bernardi, G., Olofsson, B., Filipski, J., 1985. The mosaic genome of warm-blooded vertebtates. Science, 228:953-958.

[7] Berthelsen, C.L., Glazier, J.A., Skolnick, M.H., 1992. Global fractal dimension of human DNA sequences treated as pseudorandom walks. Phys. Rev., A45:8902-8913.

[8] Bhry, T., Cziryk, A., Vicsek, T., Major, B., 1998. Application of vector space techniques to DNA. Fractals, 6:205-210.

[9] Buldyrev, S.V., Dokholyan, N.V., Goldberger, A.L., Havlin, S., Peng, C.K., Stanley, H.E., Viswanathan, G.M., 1998. Analysis of DNA sequences using methods of statistical physics. Physica, A249:430-438.

[10] Bulmer, M., 1987. A statistical analysis of nucleotide sequences of introns and exons in human genes. Mol. Biol. Evol., 4:395-405.

[11] Cebrat, S., Dudek, M.R., 1998. The effect of DNA phase structure on DNA walks. Eur. Phys. J., 3:271-276.

[12] Dudek, M., Cebrat, S., Kowalczuk, M., Mackiewicz, P., Nowicka, A., Mackiewicz, D., Dudkiewicz, M., 2002. Information Weights of Nucleotides in DNA Sequences. Inst. Microbiology Preprint, Cond-mat/0301371, Wroclaw, p.8.

[13] Duplij, D., Duplij, S., 2000. Symmetry analysis of genetic code and determinative degree. Biophysical Bull. Kharkov Univ., 488:60-70.

[14] Duplij, D., Duplij, S., 2001. Determinative degree and nucleotide content of DNA strands. Biophysical Bull. Kharkov Univ., 525:86-92.

[15] Duplij, D., Duplij, S., Chashchin, N., 2000. Symmetric properties of genetic code. Biopolymers and Cell, 16:449-454.

[16] Fickett, J.W., Torney, D.C., Wolf, D.R., 1992. Base compositional structure of genomes. Genomics, 13:1056-1064.

[17] Findley, G.L., Findley, A.M., McGlynn, S.P., 1982. Symmetry characteristics of the genetic code. Proc. Natl. Acad. Sci. USA, 79:7061-7065.

[18] Forger, M., Sachse, S., 1998. Lie Superalgebras and the Multiplet Structure of the Genetic Code I: Codon Representations. Inst. de Mat. e Estat, Preprint, Math-ph/9808001, Sao Paulo, p.23.

[19] Francino, M.P., Ochman, H., 1997. Strand asymmetries in DNA evolution. Trends Genet., 13:240-245.

[20] Frappat, L., Sciarrino, A., Sorba, P., 1998. A crystal base for the genetic code. Phys. Lett., A250:214-221.

[21] Gates, M.A., 1985. Simpler DNA sequence representations. Nature, 316:219.

[22] Govorun, D.N., Danchuk, V.D., Mishchuk, Y.R., Kondratyuk, I.V., Radomsky, N.F., Zheltovsky, N.V., 1992. AM1 calculation of the nucleic acid bases structure and vibrational spectra. J. Mol. Structure, 267:99-103.

[23] Hamori, E., 1985. Novel DNA sequence representations. Nature, 314:585-586.

[24] Hornos, J.E.M., Hornos, Y.M.M., 1993. Model for the evolution of the genetic code. Phys. Rev. Lett., 71:4401-4404.

[25] Karasev, V.A., 1976. Rhombic version of genetic vocabulary based on complementary of encoding nucleotides. Vest. Leningr. Univ., 1:93-97.

[26] Karasev, V.A., Sorokin, S.G., 1997. Topological structure of the genetic code. Genetika, 33:744-751.

[27] Kauffman, L.H., 1991. Knots and Physics. World Sci., Singapore.

[28] Kowalczuk, M., Mackiewicz, P., Mackiewicz, D., 2001a. DNA asymmetry and replicational mutational pressure. J. Appl. Genet., 42:553-577.

[29] Kowalczuk, M., Mackiewicz, P., Mackiewicz, D., Nowicka, A., Dudkiewicz, M., Dudek, M.R., Cebrat, S., 2001b. High correlation between the turnover of nucleotides under mutational pressure and the DNA composition. BMC evolutionary biology, 17:1-13.

[30] Lewin, B., 1983. Genes. Wiley and Sons, New York.

[31] Lobry, J.R., 1996. A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie, 78:323-326.

[32] Luo, L., Lee, W., Jia, L., Ji, F., Tsai, L., 1998. Statistical correlation of nucleotides in a DNA sequence. Phys. Rev., E58:861-871.

[33] Maslov, S.Y., 1981. On the nature of biological code and its possible evolution. Biophysics (Moscow), 26:632-635.

[34] Nakamura, Y., Gojobori, T., Ikemura, T., 2000. Codon usage tabulated from international DNA sequence databases: Status for the year 2000. Nucl. Acds. Res., 28:292.

[35] Nieselt-Struwe, K., 1997. Graphs in sequence spaces: A review of statistical geometry. Biophys. Chem., 66:111-131.

[36] Petrovskiy, I.G., 1938. On the topology of real plane algebraic curves. Ann. Math., 39:189-209.

[37] Ratner, V.A., 1985. Structure and evolution of the genetic code. Itogi Nauki i Tekhniki. Ser. Mol. Biol., 21:158-197.

[38] Rokhlin, V.A., 1974. Complex orientation of real algebraic curves. Func. Anal. Appl., 8:71-75.

[39] Rumer, U.D., 1968. Sistematics of codons in the genetic code. DAN SSSR, 183:225-226.

[40] Rumer, U.D., 1969. On codon sistematics in the genetic code. DAN SSSR, 187:937-938.

[41] Rumer, U.D., 2000. Genetic code as a system. Soros Educational J., 6:15-22.

[42] Schneider, B., Berman, H.B., 1995. Hydration of DNA bases is local. Biophysical J., 69:2661-2669.

[43] Singer, M., Berg, P., 1991. Genes and Genomes. University Science Books, Mill Valley.

[44] Skiena, S., 1990. Implementing Discrete Mathematics: Combinatorics and Graph Theory with Mathematica. Addison-Wesley, Reading.

[45] Sponer, J., Leszczynski, J., Vetterl, V., Hobza, P., 1996. Base stacking and hydrogen bonding in protonated cytosine dimer: The role of molecular ion-dipole and induction interactions. J. Biomolecular Structure and Dynamics, 13:695-705.

[46] Stent, G., Kalindar, R., 1981. Molecular Genetics. Mir, Moscow, p.487.

[47] Sueoka, N., 1995. Intrastrand parity rules of dna base composition and usage biases in synonymous codons. J. Mol. Evol., 40:318-325.

[48] Sukhodolec, V.V., 1985. A sence of the genetic code: Reconstruction of the prebiologocal evolutin stage. Genetika, 21:1589-1599.

[49] Torney, D.C., Whittaker, C.C., Xie, G., 1999. The statistical properties of human coding sequences. J. Mol. Biol., 286:1461-1469.

[50] Turaev, V.G., 1994. Quantum Invariants of Knots and 3-Manifolds. W. de Greuter, Berlin.

[51] Wu, C., 1991. DNA strand asymmetry. Nature, 352:114.

[52] Wu, Z.B., 2002. Self-similarity limits of genomic signatures. Inst. Mechanics Preprint, Cond-mat/0212091, Beijing, p.12.

[53] Yagi, M., Takeshima, Y., Wada, H., Nakamura, H., Matsuo, M., 2003. Two alternative exons can result from activation of the cryptic splice acceptor site deep within intron 2 of the dystrophin gene in a patient with as yet asymptomatic dystrophinopathy. Hum. Genet., 267:164-170.

[54] Yčac, M., 1969. The Biological Code. North-Holland, Amsterdam.

[55] Zhang, C.T., 1997. A symmetrical theory of DNA sequences and its applications. J. Theor. Biol., 187:297-306.

[56] Zheltovsky, N.V., Samoilenko, S.A., Govorun, D.N., 1989. In Spectroscopy of Biological Molecules. Societa Editrice Esculapio, Bologna, p.159-172.

[57] Ziegler, G.M., 1995. Lectures on Polytopes. Springer-Verlag, Berlin.

Open peer comments: Debate/Discuss/Question/Opinion

<1>

Please provide your name, email address and a comment





Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - Journal of Zhejiang University-SCIENCE