Examples



mdbootstrap.com



 
Статья
2020

Bi-Stability of a Pyramidal Structure of NH2 Groups in Nitrous Bases and its Role in the Structural and Functional Organization of the Genomic DNA


V. M. KomarovV. M. Komarov, A. A. SamchenkoA. A. Samchenko
Российский физический журнал
https://doi.org/10.1007/s11182-020-02175-4
Abstract / Full Text

The influence of the stable sp3 hybrid structure of the valence amino group orbitals of nitrous bases on the initiation of the hidden structural polymorphism of the Watson–Crick base pairs is considered. The key role of differences in the polymorphism of the AT and GC pairs in the formation of structural and functional features of the genomic DNA is shown by the methods of computer chemistry and comparative genomics.

Author information
  • Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Moscow Region, RussiaV. M. Komarov & A. A. Samchenko
References
  1. R. N. Nurmukametov, V. G. Plotnikov, and D. N. Shigorin, Zh. Fiz. Khim., 40, 1154 (1966).
  2. D. N. Shigorin, Zh. Vsesouzn. Khim. Obshch. Im. D. I. Mendeleev, 20, 32 (1975).
  3. D. N. Shigorin and V. G. Plotnikov, Dokl. Akad. Nauk SSSR, 234, 121 (1977).
  4. D. N. Shigorin, Zh. Fiz. Khim., 51, 1894 (1977).
  5. V. M. Komarov, V. G. Plotnikov, and L. V. Belousova, Opt. Spektrosk., 29, 1006–1007 (1970).
  6. V. M. Komarov and V. G. Plotnikov, Teor. Eksp. Khim., 10, No. 1, 62–68 (1974).
  7. V. M. Komarov and V. G. Plotnikov, Zh. Prikl. Spektrosk., 20, No. 2, 256–260 (1974).
  8. V. M. KOmarov and V. G. Plotn., Spectrosс. Lett., 8, No. 6, 363–373 (1975).
  9. V. G. Plotnikov, B. A. Dolgikh, and V. M. Komarov, 43, No. 6, 1072–1080 (1977).
  10. E. C. Lim, ed., Excited States, Vol. 1, Academic Press, London (1974).
  11. E. C. Lim and M. Kedzierski, Chem. Phys. Lett., 20, 242 (1973).
  12. J. D. Watson and F. H. C. Crick, Nature, 171, 737–738 (1953).
  13. V. Zenger, Principles of the Structural Organization of Nucleic Acids, Mir, Moscow (1987).
  14. C. C. Wilson, Nucleic Acids Res., 15, 8577–8591 (1987).
  15. C. C. Wilson and P. Tollin, Nucleosides & Nucleotides, 6, 643–653 (1987).
  16. K. A. Marx, S. T. Hess, and R. D. Blake, J. Biomol. Struct. Dyn., 11, 057–066 (1993).
  17. K. A. Marx, Y. Zhou, and I. Q. Kishawi, J. Biomol. Struct. Dyn., 23, 429–446 (2006).
  18. K. J. Dechering, K. Cuelenaere, R. N. H. Konings, and J. A. M. Leunissen, Nucleic Acids Res., 26, 4056–4062 (1998).
  19. B. Shomer and G. Yagil, Nucleic Acids Res., 27, 4491–4480 (1999).
  20. T. Coenye and P. Vandamme, DNA Res., 12, 221–233 (2005).
  21. F. Piazza and P. Lio, Physica A, 347, 472–488 (2005).
  22. J. Subirana and X. Messenguer, J. Theor. Biol., 283, 28–34 (2011).
  23. V. M. Komarov, R. V. Polozov, and G. G. Konoplev, Nonplanar structure of amino-substituted nitrous bases, Preprint of the Scientific Center for Biological Research of the USSR Academy of Sciences, Pushchino (1989).
  24. V. M. Komarov and R. V. Polozov, Z. Naturforsch. c, 45, 1080 (1990).
  25. V. M. Komarov, R. V. Polozov, and G. G. Konoplev, J. Theor. Biol., 155, 281–294 (1992).
  26. L. M. Sverdlov, M. A. Kovner, and E. P. Krainov, Vibrational Spectra of Polyatomic Molecules [in Russian], Nauka, Moscow (1970).
  27. J. C. D. Brand, D. R. Williams, and T. J. Cook, J. Mol. Spectrosс., 20, 359–380 (1966).
  28. R. D. Brown, P. D. Godfrey, and D. B. Kleibomer, J. Mol. Spectrosс., 124, 21–33 (1987).
  29. R. D. Brown, P. D. Godfrey, D. McNaughton, and A. P. Pierlot, J. Am. Chem. Soc., 111, 2308–2310 (1989).
  30. R. D. Brown, P. D. Godfrey, D. McNaughton, and A. P. Pierlot, Chem. Phys. Lett., 156, 61–63 (1989).
  31. J. L. Alonso, I. Pena, J. Lopez, et al., Angew. Chem. Int. Ed., 48, 6141–6143 (2009).
  32. V.M. Komarov, Biophysics, 39, No. 5, 837–842 (1994).
  33. G. Herzberg, Electronic Spectra and Structure of Polyatomic Molecules [Russian translation], Mir, Moscow (1969).
  34. V. M. Komarov, Biophysics, 43, No. 6, 967–974 (1998).
  35. V. M. Komarov, J. Biol. Phys., 24, 167–184 (1999).
  36. V. M. Komarov and N. G. Mevkh, Zh. Fiz. Khim., 69, No. 8, 1419–1421 (1995).
  37. A. V. Kabanov and V. M. Komarov, Int. J. Quant. Chem., 88, 579–587 (2002).
  38. A. V. Kabanov, V. M. Komarov, L. V. Yakushevich, and A. V. Teplukhin, Int. J. Quant. Chem., 100, 595–609 (2004).
  39. P. Hobza and C. Sandorfy, J. Am. Chem. Soc., 109, 1302–1307 (1987).
  40. P. Hobza and J. Šponer, J. Chem. Rev., 99, No. 11, 3247–3276 (1999).
  41. J. R. Roscioli and D. W. Pratt, Proc. Natl. Acad. Sci. USA, 100, 13752–13754 (2003).
  42. J. J. P. Stewart, J. Comput. Chem., 10, 209 (1989).
  43. J. J. P. Stewart, J. Mol. Struct. THEOCHEM, 401, 195 (1997).
  44. A. E. Vinogradov, Nucleic Acids Res., 31, 1838–1844 (2003).
  45. H. Nishida, Curr. Issues Mol. Biol., 15, 19–24 (2013).
  46. H. Wu, Z. Zhang, S. Hu, and J. Yu, Biology Direct., 7, No. 2, 1–16 (2012).
  47. M. D. Frank-Kamenetskii, Biopolymers, 10, 2623–2624 (1971).
  48. H. Musto, H. Naya, A. Zavala, et al., FEBS Lett., 573, 73–77 (2004).
  49. C. E. Singer and B. N. Ames, Science, 170, 822–825 (1970).
  50. H. Musto, H. Naya, A. Zavala, et al., Biochem. Biophys. Res. Commun., 347, 1–3 (2006).
  51. J. L. Oliver and A. Marin, J. Mol. Evol., 43, 216–223 (1996).
  52. N. Sueoka, J. Mol. Evol., 37, 137–153 (1993).
  53. G. Kudla, L. Lipinski, F. Caffin, et al., PLOS Biol., 4, e180 (2006).
  54. K. U. Foerstner, C. von Mering, S. D. Hooper, and P. Bork, EMBO Rep., 6, 1208–1213 (2005).
  55. B. I. Verkin, I. K. Yanson, L. F. Sukhodub, and A. B. Teplitskii, Interaction of Biomolecules [in Russian], Naukova Dumka, Kiev (1985).
  56. D. W. Ussery, T. M. Wassenaar, and S. B. Borini, Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists, Springer Verlag, London (2009).
  57. J. D. Watson, Molecular Biology of the Gene, W. A. Benjamin, Inc., New York; Amsterdam (1965).
  58. S. Karlin and J. Mrazek, Proc. Natl. Acad. Sci. USA, 94, 10227–10232 (1997).
  59. W. L. Hamilton, A. Claessens, T. D. Otto, et al., Nucleic Acids Res., 45, No. 4, 1889–1901 (2017).
  60. J. A. Subirana and X. Messeguer, Nucleic Acids Res., 38, No. 4, 1172–1181 (2010).
  61. G. Yagil, J. Mol. Evol., 37, 123–130 (1993).
  62. G. Yagil, Genomics, 87, 591–597 (2006).
  63. B. Shomer and G. Yagil, Nucleic Acids Res., 27, 4491–4480 (1999).
  64. http://www.ncbi.nlm.nih.gov/genbank.
  65. A. A. Samchenko, S. S. Kiselev, A. V. Kabanov, et al., Biophysics, 61, No. 6, 1045–1058 (2016).
  66. S. S. Kiselev, V. M. Komarov, I. S. Masulis, and O. N. Ozolin, Komp’yut. Issled. Model., 2, No. 2, 183–187 (2010).
  67. V. M. Schaibley, M. Zawistowski, D. Wegman, et al., Genome Res., 23, 1974–1984 (2013).
  68. S. Glemin, Y. Clement, J. David, and A. Ressayre, Trends Genet., 30, No. 7, 263–270 (2014).
  69. V. M. Komarov, A. A. Samchenko, and M. S. Kondrat’ev, in: Reports of Int. Conf. “Mathematical Biology and Bioinformatics,” V. D. Lakhno, ed. Pushchino, Vol. 7, Article e103 (2018), https://doi.org/10.17537/icmbb18.114.
  70. P. M. Sharp and W.-H. Li, Nucleic Acids Res., 15, No. 3, 1281–1295 (1987).
  71. Y. Narakuma, T. Gojobori, and T. Ikemura, Nucleic Acids Res., 28, 292 (2000).