Abstract
The comparative analysis of the frequency of oligomeric W- and S-tracts was conducted in the genomes of different eukaryotic species that differ in their GC-composition. The domination of mononucleotide and mixed (A/T) n -sequences compared with (G/C) n -sequences was detected in the studied eukaryotic genomes, including Dictyostelium discoideum (GC ~ 25.7%), Caenorhabditis elegans (GC ~ 36.9%), Arabidopsis thaliana (GC ~ 38.0%), Drosophila melanogaster (GC ~ 38.8%), Homo sapiens (GC ~ 40.0%), Gallus gallus (GC ~ 50.0%), Leishmania major (GC ~ 59.1%). Using the results of quantum–chemical calculations, a theoretical rationale of the important role of existing differences in the initial hidden structural polymorphism of the hydrogen bonding of the Watson–Crick AT and GC pairs in the development of this phenomenon is given. It is concluded that a decreased structural polymorphism of AT pairs compared with the high fourfold polymorphism of the main state of GC pairs may be the most probable source of the preference and reliability of the “use” of AT pairs by nature in genomic DNA of many species.
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Y. Zhou, J. W. Bizzaro, and K. A. Marx, BMC Genomics 5, 95 (2004).
A. Eyre-Walker and L. D. Hurst, Nat. Rev. Genet. 2 (7), 549 (2001).
J. Bohlin, E. Skjerve, and D. W. Ussery, PLoS Comput. Biol. 4 (4), e1000057 (2008)
C. E. Singer and B. N. Ames, Science 170, 822 (1970).
H. Musto, H. Naya, A. Zavala, et al., FEBS Lett. 573, 73 (2004).
H. Musto, H. Naya, A. Zavala, et al., Biochem. Biophys. Res. Commun. 347, 1 (2006).
J. L. Oliver and A. Marin, J. Mol. Evol. 43, 216 (1996).
K. U. Foerstner, C. von Mering, S. D. Hooper, and P. Bork, EMBO Rep. 6, 1208 (2005).
N. Sueoka, J. Mol. Evol. 37, 137 (1993).
G. Kudla, L. Lipinski, F. Caffin, et al., PLoS Biol. 4, e180 (2006).
H. Nishida, Curr. Issues Mol. Biol. 15, 19 (2013).
H. Wu, Z. Zhang, S. Hu, and J. Yu, Biol. Direct 7 (2), 1 (2012).
D. W. Ussery, T. M. Wassenaar, and S. B. Borini, Computing for Comparative Microbial Genomics (Springer-Verlag, London, 2009).
S. Karlin and J. Mrazek, Proc. Natl. Acad. Sci. USA. 94, 10227 (1997).
G. Bernardi, Structural and Evolutionary Genomics. Natural Selection in Genome Evolution (Elsevier, Amsterdam, 2004).
A. Cornish-Bowden, Nucleic Acids Res. 13, 3021 (1985).
K. A. Marx, S. T. Hess, and R. D. Blake, J. Biomol. Struct. Dyn. 11, 57 (1993).
T. Coenye and P. Vandamme, DNA Res. 12, 221 (2005).
J. A. Subirana and X. Messeguer, J. Theor. Biol. 283, 28 (2011).
K. A. Marx, Y. Zhou, and I. Q. Kishawi, J. Biomol. Struct. Dyn. 23, 429 (2006).
J. A. Subirana and X. Messeguer, Nucleic Acids Res. 38 (4), 1172 (2010)
G. Yagil, J. Mol. Evol. 37, 123 (1993).
G. Yagil, Genomics 87, 591 (2006).
B. Shomer and G. Yagil, Nucleic Acids Res. 27, 4491 (1999).
S. S. Kiselev, V. M. Komarov, I. S. Masulis, and O N. Ozolin’, Komp’yut. Issled. Model. 2 (2), 183 (2010).
S. S. Kiselev, Candidate’s Dissertation in Biology (Pushchino, 2012).
F. Piazza and P. Lio, Physica A 347, 472 (2005).
K. J. Dechering, K. Cuelenaere, R. N. H. Konings, and J. A. M. Leunissen, Nucleic Acids Res. 26, 4056 (1998).
V. M. Komarov and N. G. Mevkh, Zh. Phys. Khim. 69 (8), 1419 (1995).
V. M. Komarov, Biophysics (Moscow) 43 (6), 917 (1998).
V. M. Komarov, J. Biol. Phys. 24, 167 (1999).
A. V. Kabanov and V. M. Komarov, Int. J. Quantum Chem. 88 (5), 579 (2002).
http://www.ncbi.nlm.nih.gov/genbank/
ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens.
V. Murray, Comput. Biol. Chem. 54, 13 (2015).
E. A. Worthey, A. Schnaufer, G. Aggarwal, et al., Nucleic Acids Res. 31 (14), 4201 (2003).
R. D. Brown, D. N. Godfrey, D. McNaughton, and A. P. Pierlot, J. Am. Chem. Soc. 111, 2308 (1989).
R. D. Brown, D. N. Godfrey, D. McNaughton, and A. P. Pierlot, Chem. Phys. Lett. 156, 61 (1989).
V. M. Komarov and R. V. Polozov, Biofizika 35 (2), 367 (1990).
J. Sponer and P. Hobza, J. Phys. Chem. 98, 3161 (1994).
J. Sponer and P. Hobza, Int. J. Quant. Chem. 57, 959 (1996).
V. M. Komarov and R. V. Polozov, Z. Natuforsch. 42c, 1080 (1990).
V. M. Komarov, R. V. Polozov, and G. G. Konoplev, J. Theor. Biol. 155, 281 (1992).
V. M. Komarov, A. V. Kabanov, Yu. A. Lazarev, and A. V. Shapovalov, Matemat. Komp’yut. Obpaz. 6 (2), 405 (1999).
P. Hobza and C. Sandorfy, J. Am. Chem. Soc. 109, 1302 (1987)
C. C. Wilson, Nucleic Acids Res. 15, 8577 (1987).
C. C. Wilson and P. Tollin, Nucleosides Nucleotides 6, 643 (1987).
C. C. Wilson, Nucleosides Nucleotides 9, 479 (1990).
J. Jursa and J. Kypr, Gen. Physiol. Biophys. 12 (5), 401 (1993).
J. R. Roscioli and D. W. Pratt, Proc. Natl. Acad. Sci. USA. 100, 13752 (2003).
http://classic.chem.msu.su/gran/gamess/.
P. Hobza and J. Poner, Chem. Rev. 99 (11), 3247 (1999).
V. I. Danilov and V. M. Anisimov, Biopolym. Cell. 20 (1–2), 71 (2004).
V. I. Danilov, D. M. Hovorun, and N. Kurita, Biopolim. Klitina 21 (1), 70 (2005).
A. R. Srinivasan, R. R. Sauers, M. O. Fenley, et al., Biophys. Rev. 1, 13 (2009).
V. M. Komarov, Biophysics 43 (6), 917 (1998).
V. M. Schaibley, M. Zawistowski, D. Wegmann, et al., Genome Res. 23, 1974 (2013).
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Original Russian Text © A.A. Samchenko, S.S. Kiselev, A.V. Kabanov, M.S. Kondratjev, V.M. Komarov, 2016, published in Biofizika, 2016, Vol. 61, No. 6, pp. 1045–1058.
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Samchenko, A.A., Kiselev, S.S., Kabanov, A.V. et al. On the nature of the domination of oligomeric (dA:dT) n tracts in the structure of eukaryotic genomes. BIOPHYSICS 61, 813–824 (2016). https://doi.org/10.1134/S0006350916060233
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DOI: https://doi.org/10.1134/S0006350916060233