Abstract
The propagation, or movement, of a conformational kink along a linear structure can occur in capture, transfer, or multireflection modes. Here we use a model for two-component bistable polymer molecules with energetically non-equivalent stable states to model the propagation of the DNA transcription bubble via movement of a non-linear longitudinal stretching region along the DNA chain. We show that under certain conditions the longitudinal excitation can act as a reflector for a conformational kink and, furthermore, that conformational switching may propagate in a multireflection mode alongside conformational kink transition and conformational kink trapping.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Di Garbo A (2013) Longitudinal displacements of base pairs in DNA and effects on the dynamics of nonlinear excitations. Math Biosci 245:70–75. doi:10.1016/j.mbs.2013.03.010
Di Garbo A (2016) Anharmonic longitudinal motion of bases and dynamics of nonlinear excitation in DNA. Biophys Chem 208:76–83. doi:10.1016/j.bpc.2015.09.006
Englander SW, Kallenbach NR, Heeger AJ, Krumhansl JA, Litwin S (1980) Nature of the open state in long polynucleotide double helices: the possibility of soliton excitations. Proc Natl Acad Sci USA 77:7222–7226. doi:10.1073/pnas.77.12.7222
Lindsay SM, Powell J, Clementi E, Sarma RH (eds) (1983) Structure and dynamics nucleic acids and proteins. Adenine Press, New York, pp 241–259
Manevich LI, Savin AV (1995) Soliton mechanism for propagation of endothermal structural transitions in bistable systems. JETP 80:706–712
Manevich LI, Savin AV, Smirnov VV, Volkov SN (1994) Solitons in nondegenerate bistable systems. Phys Uspekhi 37:859–879. doi:10.1070/PU1994v037n09ABEH000043
Muto V, Lomdahl PS, Christiansen PL (1990) Two-dimensional discrete model for DNA dynamics: longitudinal wave propagation and denaturation. Phys Rev A 42:7452–7458. doi:10.1103/PhysRevA.42.7452
Poltev VI, Shulyupina NV (1986) Simulation of interactions between nucleic acid bases by refined atom-atom potential functions. J Biomol Struct Dyn 3:739–765. doi:10.1080/07391102.1986.10508459
Shikhovtseva ES, Nazarov VN (2007) Effect of the nonlinear longitudinal compression on the conformational dynamics of the bistable quasi-one-dimensional macromolecules. JETP Lett 86:497–501. doi:10.1134/S0021364007200015
Shikhovtseva ES, Nazarov VN (2013) Dynamics of conformational switchings of bistable quasi-one-dimensional macromolecules with nonlinear longitudinal stretching present. J Phys A Math Theor 46:225202. doi:10.1088/1751-8113/46/22/225202
Shikhovtseva ES, Nazarov VN (2016) Non-linear longitudinal compression effect on dynamics of the transcription bubble in DNA. Biophys Chem 214–215:47–53. doi:10.1016/j.bpc.2016.05.005
Sponer J, Leszczynski J, Hobza P (1996) Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-boned base pairs. J Phys Chem 100:5590–5596. doi:10.1021/jp953306e
Yomosa S (1983) Soliton excitations in deoxyribonucleic acid (DNA) double helices. Phys Rev A 27:2120–2125. doi:10.1103/PhysRevA.27.2120
Yomosa S (1984) Solitary excitations in deoxyribonuclei acid (DNA) double helices. Phys Rev A 30:474–490. doi:10.1103/PhysRevA.30.474
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Shikhovtseva, E.S., Nazarov, V.N. Multireflection propagation of conformational kinks in a two-component model of DNA as the transfer mode of the transcriptional replication fork. Eur Biophys J 47, 69–74 (2018). https://doi.org/10.1007/s00249-017-1230-x
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-017-1230-x