Understanding the self-assembly dynamics of A/T absent 'four-way DNA junctions with sticky ends' at altered physiological conditions through molecular dynamics simulations.

Autor: Singh A; Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India., Yadav RK; Department of Physics, B.R.D. Post Graduate College, Deoria, India., Shati A; Department of Biology, Faculty of Science, King Khaild University, Abha, Saudi Arabia., Kamboj NK; School of Physical Sciences, DIT University, Dehradun, Uttarakhand, India., Hasssan H; Department of Pathology, College of Medicine, King Khaild University, Abha, Saudi Arabia.; Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt., Bharadwaj S; Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea., Rana R; Department of Research, Sir Ganga Ram Hospital, New Delhi, India., Yadava U; Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2023 Feb 08; Vol. 18 (2), pp. e0278755. Date of Electronic Publication: 2023 Feb 08 (Print Publication: 2023).
DOI: 10.1371/journal.pone.0278755
Abstrakt: Elucidation of structure and dynamics of alternative higher-order structures of DNA such as in branched form could be targeted for therapeutics designing. Herein, we are reporting the intrinsically dynamic and folds transitions of an unusual DNA junction with sequence d(CGGCGGCCGC)4 which self-assembles into a four-way DNA junction form with sticky ends using long interval molecular simulations under various artificial physiological conditions. The original crystal structure coordinates (PDB ID: 3Q5C) for the selected DNA junction was considered for a total of 1.1 μs molecular dynamics simulation interval, including different temperature and pH, under OPLS-2005 force field using DESMOND suite. Following, post-dynamics structure parameters for the DNA junction were calculated and analyzed by comparison to the crystal structure. We show here that the self-assembly dynamics of DNA junction is mitigated by the temperature and pH sensitivities, and discloses peculiar structural properties as function of time. From this study it can be concluded on account of temperature sensitive and pH dependent behaviours, DNA junction periodic arrangements can willingly be synthesized and redeveloped for multiple uses like genetic biomarkers, DNA biosensor, DNA nanotechnology, DNA Zipper, etc. Furthermore, the pH dis-regulation behaviour may be used to trigger the functionality of DNA made drug-releasing nanomachines.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Singh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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