311
Views
16
CrossRef citations to date
0
Altmetric
Articles

Compensatory nature of Chargaff’s second parity rule

&
Pages 1324-1336 | Received 02 May 2012, Accepted 24 Sep 2012, Published online: 12 Nov 2012

References

  • Albrecht-Buehler, G. (2006). Asymptotically increasing compliance of genomes with chargaff’s second parity rules through inversions and inverted transpositions. Proceedings of the National Academy of Sciences, 103, 17828–17833.
  • Baisnée, P. F., Hampson, S., & Baldi, P. (2002). Why are complementary DNA strands symmetric? Bioinformatics, 18, 1021–1033.
  • Bell, S. J., & Forsdyke, D. R. (1999). Accounting units in DNA. Journal of Theoretical Biology, 197, 51–61.
  • Bell, S. J., & Forsdyke, D. R. (1999). Deviations from Chargaff’s second parity rule correlate with direction of transcription. Journal of Theoretical Biology, 197, 63–76.
  • Eckert, K. A., & Kunkel, T. A. (1991). DNA polymerase fidelity and the polymerase chain reaction. Genome Research, 1, 17–24.
  • Fickett, J. W., Torney, D. C., & Wolf, D. R. (1992). Base compositional structure of genomes. Genomics, 13, 1056–1064.
  • Forsdyke, D. R. (1995). A stem-loop “kissing” model for the initiation of recombination and the origin of introns. Molecular Biology and Evolution, 12, 949–958.
  • Forsdyke, D. R. (1995). Relative roles of primary sequence and (g+c)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. Journal of Molecular Evolution, 41, 573–581.
  • Forsdyke, D. R. (2006). Evolutionary Bioinformatics. New York, NY: Springer Verlag.
  • Forsdyke, D. R., & Bell, S. J. (2004). Purine-loading, stem-loops, and chargaff’s second parity rule. Applied Bioinformatics, 3, 3–8.
  • Forsdyke, D. R., Zhang, C., & Wei, J.-F. (2010). Chromosomes as independent accounting units. The assigned orientation of C. elegans chromosomes minimizes the total W-base Chargaff difference. Journal of Biological Systems, 18, 1–16.
  • Francino, M. P., & Ochman, H. (1997). Strand asymmetries in DNA evolution. Trends in Genetics, 13, 240–245.
  • Freeman, J. M., Plasterer, T. N., Smith, T. F., & Mohr, S. C. (1998). Patterns of Genome Organization in Bacteria. Science, 279, 1827–1830.
  • Frenkel, Z. M., & Trifonov, E. N. (2012). Origin and evolution of genes and genomes. Crucial role of triplet expansions. Journal of Biomolecular Structure & Dynamics, 30, 201–210.
  • Gabdank, I., Barash, D., & Trifonov, E. N. (2009). Nucleosome DNA bendability matrix (C. elegans). Journal of Biomolecular Structure & Dynamics, 26, 403–412.
  • Jurka, J. (2000). Repbase update: A database and an electronic journal of repetitive elements. Trends in Genetics, 16, 418–420.
  • Karolchik, D., Hinrichs, A. S., Furey, T. S., Roskin, K. M., Sugnet, C. W., Haussler, D., & Kent, W. J. (2004). The UCSC table browser data retrieval tool. Nucleic Acids Research, 32, D493–D496.
  • Kuhn, R. M., Karolchik, D., Zweig, A. S., Wang, T., Smith, K. E., Rosenbloom, K. R., & Kent, W. J. (2009). The UCSC genome browser database: Update 2009. Nucleic Acids Research, 37, D755–D761.
  • Kunz, B. A., & Kohalmi, S. E. (1991). Modulation of mutagenesis by deoxyribonucleotide levels. Annual Reviews of Genetics, 25, 339–359.
  • Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., & Morgan, M. J. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921.
  • Lewis, S. E., Searle, S. M. J., Harris, N., Gibson, M., Iyer, V., Richter, J., & Clamp, M. E. (2002). Apollo: A sequence annotation editor. Genome Biology, 3, 1–0082.
  • Lobry, J. R. (1996). A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie, 78, 323–326.
  • Lobry, J. R. (1999). A nice wrong model for the evolution of DNA base frequencies. Physica A: Statistical Mechanics and its Applications, 273, 99–102.
  • Mirkin, E. V., & Mirkin, S. M. (2005). Mechanisms of transcription-replication collisions in bacteria. Molecular and cellular biology, 25, 888–895.
  • Mitchell, D., & Bridge, R. (2006). A test of Chargaff’s second rule. Biochemical and Biophysical Research Communications, 340, 90–94.
  • Mrazek, J., & Karlin, S. (1998). Strand compositional asymmetry in bacterial and large viral genomes. Proceedings of the National Academy of Sciences, 95, 3720–3725.
  • Nikolaou, C., & Almirantis, Y. (2005). A study on the correlation of nucleotide skews and the positioning of the origin of replication: Different modes of replication in bacterial species. Nucleic Acids Research, 33, 6816–6822.
  • Okamura, K., Wei, J., & Scherer, S. (2007). Evolutionary implications of inversions that have caused intra-strand parity in DNA. Bmc Genomics, 8, 160–166.
  • Prabhu, V. V. (1993). Symmetry observations in long nucleotide sequences. Nucleic Acids Research, 21, 2797–2800.
  • Qi, D., & Cuticchia, A. J. (2001). Compositional symmetries in complete genomes. Bioinformatics, 17, 557–559.
  • Rapoport, A. E., Frenkel, Z. M., & Trifonov, E. N. (2011). Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. Journal of Biomolecular Structure & Dynamics, 28, 567–574.
  • Rapoport, A. E., & Trifonov, E. N. (2011). “Anticipated” nucleosome positioning pattern in prokaryotes. Gene, 488, 41–45.
  • Rocha, E. P. C. (2002). Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends in Microbiology, 10, 393–395.
  • Rocha, E. P. C. (2004). The replication-related organisation of the bacterial chromosome. Microbiology, 150, 1609–1627.
  • Shannon, C. E. (1948). A mathematical theory of communication. Bell System Technical Journal, 27, 379–423.
  • Smit, A. F. A. (1999). Interspersed repeats and other mementos of transposable elements in mammalian genomes. Current Opinion in Genetics and Development, 9, 657–663.
  • Sueoka, N. (1995). Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. Journal of Molecular Evolution, 40, 318–325.
  • Szybalski, W., Kubinski, H., & Sheldrick, P. (1966). Pyrimidine clusters on the transcribing strands of DNA and their possible role in the initiation of RNA synthesis. Cold Spring Harbour Symposium on Quantitative Biology, 31, 123–127.
  • Tillier, E. R. M., & Collins, R. A. (2000). The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. Journal of Molecular Evolution, 50, 249–257.
  • Trifonov, E. N. (2010). Base pair stacking in nucleosome DNA and bendability sequence pattern. Journal of Theoretical Biology, 263, 337–339.
  • Trifonov, E. N., & Bettecken, T. (1997). Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene, 205, 1–6.
  • Vartanian, J.-P., Meyerhans, A., Sala, M., & Wain-Hobson, S. (1994). G -> A hypermutation of the human immunodeficiency virus type 1 genome: Evidence for dCTP pool imbalance during reverse transcription. Proceedings of the National Academy of Sciences, 91, 3092–3096.
  • Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., & Zody, M. C. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520–562.
  • Zeigler, D. R., & Dean, D. H. (1990). Orientation of genes in the bacillus subtilis chromosome. Genetics, 125, 703–708.
  • Zhang, C. T., Zhang, R., & Ou, H. Y. (2003). The z curve database: A graphic representation of genome sequences. Bioinformatics, 19, 593–599.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.