Mathematical Biology & Bioinformatics | Volume 14 Issue 1 Year 2019

Yakushevich L.V.¹, Krasnobaeva L.A.^{2, 3}

Plasmid pBR322 and Nonlinear Conformational Distortions (Kinks)

Mathematical Biology & Bioinformatics. 2019;14(1):327-339.

doi: 10.17537/2019.14.327.

References

Englander S.W., Kallenbach N.R., Heeger A.J., Krumhansl J.A., Litwin A. Nature of the open state in DNA structure. Proc. Natl. Acad. Sci. 1980;77:7222–7226.
Clark D., Pazdernik N. Biotechnology. 2nd Edition. Academic Cell, 2015.
Zuo Y., Steitz T.A. A structure-based kinetic model of transcription. Transcription. 2017;8:1–8. doi: 10.1080/21541264.2016.1234821
He Y., Yan C., Fang J., Inouye C., Tjian R., Ivanov I., Nogales E. Near-atomic resolution visualization of human transcription promoter opening. Nature. 2016;533:359–365. doi: 10.1038/nature17970
Bailey L.J., Doherty A.J. Mitochondrial DNA replication: a PrimPol perspective. Biochem Soc Trans. 2017;45:513–529. doi: 10.1042/BST20160162
Bleichert F, Botchan M.R., Berger J.M. Mechanisms for initiating cellular DNA replication. Science. 2017;355:215–222. doi: 10.1126/science.aah6317
Sicard F., Destainville N., Manghi M. DNA denaturation bubbles: Free-energy landscape and nucleation/closure rates. J. of Chemical Physics. 2015;142:903–910. doi: 10.1063/1.4905668
Shi C., Shang F., Zhou M., Zhang P., Wang Y., Ma C. Triggered isothermal PCR by denaturation bubble-mediated strand exchange amplification. Chem. Commun. 2016;52:11551–11554. doi: 10.1039/C6CC05906F
Singh A.R., Granek R. Manipulation of double-stranded DNA melting by force. Phys. Rev. E. 2017;96:032417–032422. doi: 10.1103/PhysRevE.96.032417
Dwiputra D., Hidayat W., Zen F.P. Nonlinear dynamics of DNA bubble induced by site specific DNA-protein interaction. J. Phys.: Conf. Ser. 2017;856:012005–012009. doi: 10.1088/1742-6596/856/1/011001
Ryasik A., Orlov M., Zykova E., Ermak T., Sorokin A. Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification. J. Bioinf. Comput. Biol. 2018;16:1840003. doi: 10.1142/S0219720018400036
Salerno M. Discrete model for DNA-promoter dynamics. Phys. Rev. A. 1991;44:5292–5297. doi: 10.1103/PhysRevA.44.5292
Yakushevich L.V., Krasnobaeva L.A., Shapovalov A.V., Quintero N.R. One- and Two-Soliton Solutions of the Sine-Gordon Equation as Applied to DNA. Biophysics. 2005;50:450–455.
Derks G., Gaeta G. A minimal model of DNA dynamics in interaction with RNA-polymerase. Physica D: Nonlinear Phenomena. 2011;240:1805–1817. doi: 10.1017/S0956792511000301
Traverso J.J., Manoranjan V.S., Bishop A.R., Rasmussen K., Voulgarakis N.K. Allostery through protein-induced DNA bubbles. Sci. Rep. 2018;5:9037–9043. doi: 10.1038/srep09037
McLaughlin D.W., Scott A.C. Perturbation analysis of fuxon dynamics. Phys. Rev. A. 1978;18:1652–1658.
Yakushevich L.V., Krasnobaeva L.A. Effects of dissipation and external fields on the dynamics of conformational distortions in DNA. Biophysics. 2007;52:237–243.
Grinevich A.A, Ryasik A.A, Yakushevich L.V. The dynamics of polynucleotide chain consisting of two different homogeneous sequences, divided by interface. Computer Research and Modeling. 2013;5:241–253.
Grinevich A.A., Ryasik A.A., Yakushevich L.V. Trajectories of DNA bubles. Chaos, Solitons & Fractals. 2015;75:62–75. doi: 10.1016/j.chaos.2015.02.009
Yakushevich L.V., Krasnobaeva L.A. Trajectories of the DNA kinks in the sequences containing CDS regions. Mathematical Biology and Bioinformatics. 2017;12:1–13. doi: 10.17537/2017.12.1
Yakushevich L.V., Krasnobaeva L.A. Analytical approaches for exploration of the dynamics of genes having one coding region. Biophysics. 2018;63:41–53. doi: 10.1134/S0006350918010190
Bolivar F, Rodriguez R.L., Greene P.J., Betlach M.C., Heyneker H.L., Boyer H.W., Crosa J.H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2:95–113. doi: 10.1016/0378-1119(77)90000-2
Watson N. A new revision of the sequence of plasmid pBR322. Gene. 1988;70:399–403. doi: 10.1016/0378-1119(88)90212-0