Russian version English version
Volume 15   Issue 1   Year 2020
Geraskin E.I.1, Lakhno V.D.2, Chetverikov A.P.1, Shigaev A.S.2

Investigation of DNA Breather Dynamics in A Model with Non-Local Inter-Site Interaction

Mathematical Biology & Bioinformatics. 2020;15(1):93-105.

doi: 10.17537/2020.15.93.


  1. Triberis G.P., Dimakogianni M. DNA in the material world: electrical properties and nano-applications. Recent Patents on Nanotechnology. 2009;3:135–153. doi: 10.2174/187221009788490040
  2. Nanobioelectronics-for Electronics, Biology, and Medicine. Eds. Offenhauser A., Rinaldi R. Springer Science & Business Media, 2009.
  3. Lakhno V.D. DNA Nanobioelectronics. International Journal of Quantum Chemistry. 2008;108:1970–1981. doi: 10.1002/qua.21717
  4. Lakhno V.D., Sultanov V.B. Baseline logical elements on the basis of DNA. International Journal of Quantum Chemistry. 2008;108:1913–1920. doi: 10.1002/qua.21690
  5. Korshunova A.N., Lakhno V.D. Rapid formation of a moving polaron state in a homogeneous molecular polynucleotide chain of finite length: Keldysh Institute preprints. 2018. No. 231. 22 p. (in Russ.). doi: 10.20948/prepr-2018-231
  6. Lakhno V.D., Korshunova A.N., Formation of stationary electronic states in finite homogeneous molecular chains. Math. Biol. Bioinf. 2010;5:1–29.
  7. Conwell E.M., Rakhmanova S.V. Polarons in DNA. Proc. Natl. Acad. Sci. 2000;97:4556–4560.
  8. Chetverikov A.P., Sergeev K.S., Lakhno V.D. Trapping and transport of charges in DNA by mobile discrete breathers. Mathematical Biology and Bioinformatics. 2018;13:1–12. doi: 10.17537/2018.13.1
  9. Chetverikov A.P., Ebeling W., Lakhno V.D., Shigaev A.S., Velarde M.G. Eur. Phys. J. B. 2016;89:101–111.
  10. Chetverikov A.P., Ebeling W., Lakhno V.D., Velarde M.G. Discrete-breather-assisted charge transport along DNA-like molecular wires. Physical Review E. 2019;100:052203. doi: 10.1103/PhysRevE.100.052203
  11. Chakraborty T. Charge Migration in DNA. Nano Science and Technology. Berlin, Heidelberg: Springer, 2007. doi: 10.1007/978-3-540-72494-0
  12. Shigaev A.S., Ponomarev O.A., Lakhno V.D. Theoretical and Experimental Investigations of DNA Open States. Mathematical Biology and Bioinformatics. 2013;8:553–664. doi: 10.17537/2013.8.553
  13. Dauxois T., Peyrard M., Bishop A.R. Entropy-driven DNA denaturation. Physical Review E. 1993;47:R44–R47. doi: 10.1103/PhysRevE.47.R44
  14. Tewari A.K., Dubey R. Emerging trends in molecular recognition: utility of weak aromatic interactions. Bioorganic & Medicinal Chemistry. 2008;16:126–143. doi: 10.1016/j.bmc.2007.09.023
  15. Gago F. Stacking Interactions and Intercalative DNA Binding. Methods. 1998;14:277–292. doi: 10.1006/meth.1998.0584
  16. Ares S., Kalosakas G. Distribution of Bubble Lengths in DNA. Nano Letters. 2007;7:307–311. doi: 10.1021/nl062304a
  17. Choi C.H., Kalosakas G., Rasmussen K.O., Hiromura M., Bishop A.R., Usheva A. DNA dynamically directs its own transcription initiation. Nucleic Acids Research. 2004;32:1584–1590. doi: 10.1093/nar/gkh335
  18. Kalosakas G., Rasmussen K.O., Bishop A.R., Choi C.H., Usheva A. Sequence-specific thermal fluctuations identify start sites for DNA transcription. Europhysics Letters. 2004;68:127–133. doi: 10.1209/epl/i2004-10167-8
  19. Alexandrov B.S., Gelev V., Monisova Y., Alexandrov L.B., Bishop A.R., Rasmussen K.O., Usheva A. A nonlinear dynamic model of DNA with a sequence-dependent stacking term. Nucleic Acids Research. 2009;37:2405–2410. doi: 10.1093/nar/gkp016
  20. Alexandrov B.S., Gelev V., Yoo S.W., Alexandrov L.B., Fukuyo Y., Bishop A.R., Rasmussen K.O., Usheva A. DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation. Nucleic Acids Research. 2010;38:1790–1795. doi: 10.1093/nar/gkp1084
  21. Alexandrov B.S., Valtchinov V.I., Alexandrov L.B., Gelev V., Dagon Y., Bock J., Kohane I.S., Rasmussen K.O., Bishop A.R., Usheva A. DNA Dynamics Is Likely to Be a Factor in the Genomic Nucleotide Repeats Expansions Related to Diseases. PLoS One. 2011;6:1–6. doi: 10.1371/annotation/f68e9b71-cae1-4f9c-9308-a444d3ea753d
  22. Kantorovitz M.R., Rapti Z., Gelev V., Usheva A. Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites. BMC bioinformatics. 2010;11(1):604. doi: 10.1186/1471-2105-11-604
  23. Campa A., Giansanti A. Melting of DNA oligomers: dynamical models and comparison with experimental results. Journal of biological physics. 1999;24:141–155. doi: 10.1023/A:1005166612156
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2020.15.93
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


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