Russian version English version
Volume 15   Issue 2   Year 2020
Shigaev A.S., Lihachev I.V., Lakhno V.D.

DNA Model with Non-Local Inter-Site Interaction in Collisional Thermostat

Mathematical Biology & Bioinformatics. 2020;15(2):129-137.

doi: 10.17537/2020.15.129.

References

  1. Shigaev A.S., Ponomarev O.A., Lakhno V.D. Theoretical and Experimental Investigations of DNA Open States. Mathematical Biology and Bioinformatics. 2013;8(2):553–664. doi: 10.17537/2013.8.553
  2. Feklistov A., Darst S.A. Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit. Cell. 2011;147:1257–1269. doi: 10.1016/j.cell.2011.10.041
  3. Liu X., Bushnell D.A., Kornberg R.D. Lock and key to transcription: sigma-DNA interaction. Cell. 2011;147:1218–1219. doi: 10.1016/j.cell.2011.11.033
  4. Dauxois T., Peyrard M., Bishop A.R. Entropy-driven DNA denaturation. Physical Review E. 1993;47:R44–R47. doi: 10.1103/PhysRevE.47.R44
  5. Ting J.J.-L., Peyrard M. Effective breather trapping mechanism for DNA transcription. Physical Review E. 1996;53:1011–1020. doi: 10.1103/PhysRevE.53.1011
  6. Larsen P.V., Christiansen P.L., Bang O., Archilla J.F.R., Gaididei Yu.B. Energy funneling in a bent chain of Morse oscillators with long-range coupling. Physical Review E. 2004;69. Article No. 026603. doi: 10.1103/PhysRevE.69.026603
  7. Ares S., Kalosakas G. Distribution of Bubble Lengths in DNA. Nano Letters. 2007;7:307–311. doi: 10.1021/nl062304a
  8. Kochoyan M., Leroy J.L., Gueron M. Proton Exchange and Base-pair Lifetimes in a Deoxy-duplex Containing a Purine-Pyrimidine Step and in the Duplex of Inverse Sequence. Journal of Molecular Biology. 1987;196:599–609. doi: 10.1016/0022-2836(87)90036-2
  9. Campa A., Giansanti A. Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains. Physical Review E. 1998;58:3585–3588. doi: 10.1103/PhysRevE.58.3585
  10. 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
  11. Gago F. Stacking Interactions and Intercalative DNA Binding. Methods. 1998;14:277–292. doi: 10.1006/meth.1998.0584
  12. Geraskin E.I.1, Lakhno V.D., Chetverikov A.P., Shigaev A.S. Investigation of DNA Breather Dynamics in A Model with Non-Local Inter-Site Interaction. Mathematical Biology and Bioinformatics. 2020;15(1):93–105. doi: 10.17537/2020.15.93
  13. Balabaev N.K., Lemak A.S. Molecular-dynamics of linear polymer in hydrodynamic flow. J. Phys. Chem. 1995;69:28–32.
  14. Lemak A. S., Balabaev N. K. A comparison between collisional dynamics and brownian dynamics. Molecular Simulation. 1995;15:223–231. doi: 10.1080/08927029508022336
  15. Lemak A.S., Balabaev N.K. Molecular dynamics simulation of polymer chain in solution by collisional dynamics method. J. Comput. Chem. 1996;17:1685-1695. doi: 10.1002/(SICI)1096-987X(19961130)17:15<1685::AID-JCC1>3.0.CO;2-L
  16. 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
  17. Likhachev I.V., Lakhno V.D. Investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method. arXiv: 1811.03405 [cond-mat.soft]. 2018. 6 p. doi: 10.1016/j.cplett.2019.04.027.
  18. Likhachev I.V., Lakhno V.D. The direct investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method. Chemical Physics Letters. 2019;727:55–58. doi: 10.1016/j.cplett.2019.04.027
  19. Likhachev I.V., Lakhno V.D. Investigation of DNA denaturation in Peyrard-Bishop-Dauxoismodel by molecular dynamics method. Eur. Phys. J. B. 2019;92:253. doi: 10.1140/epjb/e2019-90741-6
  20. Leijon M., Graslund A. Effects of sequence and length on imino proton exchange and base pair opening kinetics in DNA oligonucleotide duplexes. Nucleic Acids Research. 1992;20:5339–5343. doi: 10.1093/nar/20.20.5339
  21. Nonin S., Leroy J.L., Gueron M. Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying. Biochemistry. 1995;34:10652–10659. doi: 10.1021/bi00033a041
  22. Sadovnichy V., Tikhonravov A., Voevodin Vl., Opanasenko V. "Lomonosov": Supercomputing at Moscow State University. In: Contemporary High Performance Computing: From Petascale toward Exascale. Ed. Vetter J.S. Boca Raton, USA: CRC Press, 2013. P. 283–307.
Table of Contents Original Article
Math. Biol. Bioinf.
2020;15(2):129-137
doi: 10.17537/2020.15.129
published in Russian

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

 

  Copyright IMPB RAS © 2005-2022