Advanced search
Publication Cover
Journal of Biomolecular Structure and Dynamics Volume 39, 2021 - Issue 6
Journal homepage
78
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Hybridization kinetics of DNA fragments in the presence of ligands intercalating into DNA-duplexes

Valeri B. Arakelyana Faculty of Physics, Department of Molecular Physics, Yerevan State University, Yerevan, ArmeniaView further author information
,
Aleksandr Y. Mamasakhlisovb Institute of Mathematics and High Technologies, Department of General Physics and Quantum Nano-structures, Russian-Armenian (Slavonic) University, Yerevan, ArmeniaView further author information
,
Eduard M. Kazaryanb Institute of Mathematics and High Technologies, Department of General Physics and Quantum Nano-structures, Russian-Armenian (Slavonic) University, Yerevan, ArmeniaView further author information
,
Marine A. Parsadanyanc Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, ArmeniaView further author information
&
Poghos O. Vardevanyanc Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, ArmeniaCorrespondence[email protected]
View further author information
Pages 1907-1911 | Received 24 Feb 2020, Accepted 03 Mar 2020, Published online: 16 Mar 2020

References

  • Arakelyan, V., Babayan, Y., & Potikyan, G. (2000). Determination of constant rates of adsorption of ligand on DNA: Analysis of correlation functions. Journal of Biomolecular Structure and Dynamics, 18(2), 231–235. doi:10.1080/07391102.2000.10506661
  • Arakelyan, V. B., Babayan, S. Y., Tairyan, V. I., Arakelyan, A. V., Parsadanyan, M. A., & Vardevanyan, P. O. (2006). Kinetics of ligand binding to nucleic acids. Journal of Biomolecular Structure and Dynamics, 23, 479–483. doi:10.1080/07391102.2006.10507073
  • Ghazaryan, A. A., Dalyan, Y. B., Haroutiunian, S. G., Tikhomirova, A., Taulier, N., Wells, J. W., & Chalikian, T. V. (2006). Thermodynamics of Interactions of water-soluble porphyrins with RNA duplexes. Journal of the American Chemical Society, 128(6), 1914–1921. doi:10.1021/ja054070n
  • Halperin, A., Buhot, A., & Zhulina, E. B. (2004). Sensitivity, specificity, and the hybridization isotherms of DNA chips. Biophysical Journal, 86(2), 718–730. doi:10.1016/S0006-3495(04)74150-8
  • Halperin, A., Buhot, A., & Zhulina, E. B. (2005). Brush effects on DNA chips: Thermodynamics, kinetics, and design guidelines. Biophysical Journal, 89(2), 796–811. doi:10.1529/biophysj.105.063479
  • Halperin, A., Buhot, A., & Zhulina, E. B. (2006). On the hybridization isotherms of DNA microarrays: The Langmuir model and its extensions. Journal of Physics: Condensed Matter, 18, S463–S490. doi:10.1088/0953-8984/18/18/S01
  • Kitahara, K., Horsthemke, W., Lefever, R., & Inaba, Y. (1980). Phase diagrams of noise induced transitions: Exact results for a class of external coloured noise. Progress of Theoretical Physics, 64(4), 1233–1247. doi:10.1143/PTP.64.1233
  • Mamasakhlisov, Y., Sngryan, H., Tonoyan, S., Hakobyan, A., & Vardevanyan, P. (2019). The double-stranded DNA stability in presence of a flexible polymer. Journal of Biomolecular Structure and Dynamics, 37(5), 1099–1103. doi:10.1080/07391102.2018.1459320
  • Pasternack, R. F., Goldsmith, J. I., Szep, S., & Gibbs, E. J. (1998). A spectroscopic and thermodynamic study of porphyrin/DNA supramolecular assemblies. Biophysical Journal, 75(2), 1024–1031. doi:10.1016/S0006-3495(98)77591-5
  • Peterson, A. W., Heaton, R. J., & Georgiadis, R. M. (2001). The effect of surface probe density on DNA hybridization. Nucleic Acids Research, 29(24), 5163–5168. doi:10.1093/nar/29.24.5163
  • Schmitt, T. J., & Knotts, T. A. I. V. (2011). Thermodynamics of DNA hybridization on surfaces. The Journal of Chemical Physics, 134(20), 2051051–2051059. doi:10.1063/1.3592557
  • Sischka, A., Toensing, K., Eckel, R., Wilking, S. D., Sewald, N., Ros, R., & Anselmetti, D. (2005). Molecular mechanisms and kinetics between DNA and DNA binding ligands. Biophysical Journal, 88(1), 404–411. doi:10.1529/biophysj.103.036293
  • Sorokin, N. V., Chechetkin, V. R., Pan'kov, S. V., Somova, O. G., Livshits, M. A., Donnikov, M. Y., Turygin, A. Y., Barsky, V. E., & Zasedatelev, A. S. (2006). Kinetics of hybridization on surface oligonucleotide microchips: Theory, experiment, and comparison with hybridization on gel-based microchips. Journal of Biomolecular Structure and Dynamics, 24(1), 57–66. doi:10.1080/07391102.2006.10507099
  • Su, Q., Vogt, S., & Nöll, G. (2018). Langmuir analysis of the binding affinity and kinetics for surface tethered duplex DNA and a ligand-apoprotein complex. Langmuir, 34(49), 14738–14748. doi:10.1021/acs.langmuir.7b04347
  • Vardevanyan, P. O., Antonyan, A. P., Parsadanyan, M. A., & Shahinyan, M. A. (2019). Study of the influence of the ionic strength on complex-formation of ethidium bromide with poly(rA)-poly(rU). Journal of Biomolecular Structure and Dynamics, 38, 1–6. doi:10.1080/07391102.2019.1630006
  • Vardevanyan, P. O., Antonyan, A. P., Parsadanyan, M. A., Shahinyan, M. A., & Sahakyan, V. G. (2018). Peculiarities of interaction of synthetic polyribonucleotide poly(rA)-poly(rU) with some intercalators. Journal of Biomolecular Structure and Dynamics, 36(14), 3607–3613. doi:10.1080/07391102.2017.1402708
  • Vardevanyan, P. O., Antonyan, A. P., Parsadanyan, M. A., Torosyan, M. A., & Karapetian, A. T. (2016). Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters. Journal of Biomolecular Structure and Dynamics, 34(7), 1377–1382. doi:10.1080/07391102.2015.1079557
  • Watterson, J. H., Piunno, P. A. E., & Krull, U. J. (2002). Towards the optimization of an optical DNA sensor: Control of selectivity coefficients and relative surface affinities. Analytica Chimica Acta, 457(1), 29–38. doi:10.1016/S0003-2670(01)01304-6

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.