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Mishra RK, Maganti L. Antitumor drugs effect on the stability of double-stranded DNA: steered molecular dynamics analysis. J Biomol Struct Dyn 2022; 40:11373-11382. [PMID: 34355668 DOI: 10.1080/07391102.2021.1960193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Denaturation of the DNA double helix inside the cell is essential for cellular processes such as replication and transcription for the growth of the cells. However, the growth of unwanted cells, which are responsible for cancerous kind of disease, is one of the biggest challenges of modern therapeutics. DNA cross-linking agents may kill cancer cells by damaging their DNA and stopping them from dividing. In the present study, we have carried out steered molecular dynamics simulations to study the effects of rupture and unzipping forces on the stability of dsDNA in the absence and presence of covalently bonded drugs. We have found that the stability of dsDNA increases strongly in the presence of covalently bonded drugs. The microscopic study of disruption of hydrogen-bonds associated with base-pairs of the dsDNA and the study of the variation of stacking overlap parameters gives evidence of symmetry during the rupture and asymmetry in the unzip event. The significance of the mechanism of force-induced melting study of the dsDNA in the absence and presence of antitumor drugs might have a biological relevance as it provides a pathway to open the double helix in a specific position and may help for the pharmaceutical design of drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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Upadhyaya A, Nath S, Kumar S. Force-induced rupture of double-stranded DNA in the absence and presence of covalently bonded anti-tumor drugs: Insights from molecular dynamics simulations. J Chem Phys 2018; 148:215105. [DOI: 10.1063/1.5024975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Anurag Upadhyaya
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Shesh Nath
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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Affiliation(s)
- Adam K. Sieradzan
- Chemistry
Department, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Paweł Krupa
- Chemistry
Department, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - David J. Wales
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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Mishra RK, Nath S, Kumar S. Rupture of DNA aptamer: New insights from simulations. J Chem Phys 2016; 143:164902. [PMID: 26520549 DOI: 10.1063/1.4933948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules, e.g., adenosinemonophosphate and adenosinetriphosphate, form additional hydrogen bonds with base-pockets termed as "binding-pockets," which enhance the stability. Using the Langevin dynamics simulations of coarse grained model of DNA followed by atomistic simulations, we investigated the influence of base-pocket and binding-pocket on the stability of DNA aptamer. Striking differences have been reported here for the separation induced by temperature and force, which require further investigation by single molecule experiments.
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Affiliation(s)
| | - Shesh Nath
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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Kumar S, Kumar R, Janke W. Periodically driven DNA: Theory and simulation. Phys Rev E 2016; 93:010402. [PMID: 26871010 DOI: 10.1103/physreve.93.010402] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/07/2022]
Abstract
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude F and frequency ν and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis loop, A_{loop}, scales with the same exponents as observed in a recent study based on a much more detailed model. However, towards the true thermodynamic limit, the high-frequency scaling regime extends to lower frequencies for larger chain length L and the system has only one scaling (A_{loop}≈ν^{-1}F^{2}). Expansion of an analytical expression for A_{loop} obtained for the model system in the low-force regime revealed that there is a new scaling exponent associated with force (A_{loop}≈ν^{-1}F^{2.5}), which has been validated by high-precision numerical calculation. By a combination of analytical and numerical arguments, we also deduce that for large but finite L, the exponents are robust and independent of temperature and friction coefficient.
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Affiliation(s)
- Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Ravinder Kumar
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
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Mosayebi M, Louis AA, Doye JPK, Ouldridge TE. Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors. ACS NANO 2015; 9:11993-2003. [PMID: 26575598 DOI: 10.1021/acsnano.5b04726] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.
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Affiliation(s)
- Majid Mosayebi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
- School of Physics, Institute for Research in Fundamental Sciences (IPM) , Tehran 19538-33511, Iran
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford OX1 3NP, United Kingdom
- Department of Mathematics, Imperial College , 180 Queen's Gate, London SW7 2AZ, United Kingdom
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Nath S, Modi T, Mishra RK, Giri D, Mandal BP, Kumar S. Statistical mechanics of DNA rupture: theory and simulations. J Chem Phys 2014; 139:165101. [PMID: 24182082 DOI: 10.1063/1.4824796] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the literature based on the coarse-grained models (theory and simulations). We discuss the possible reasons and improve the coarse-grained model by incorporating the consequences of semi-microscopic details of the nucleotides in its description. The distributions obtained by the modified model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic simulations.
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Affiliation(s)
- S Nath
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
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Sengupta E, Yan Y, Wang X, Munechika K, Ginger DS. Dynamic force spectroscopy of photoswitch-modified DNA. ACS NANO 2014; 8:2625-2631. [PMID: 24502655 DOI: 10.1021/nn406334b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We apply a combination of photoswitch-modified DNA and AFM-based pulling measurements to study the force-induced melting of double-stranded DNA in the unzipping geometry. We measure the differences in peak rupture force for azobenzene-modified DNA, as the incorporated azobenzenes are photoswitched reversibly between the trans and the cis form. Fitting our rupture force versus loading rate data, we obtain off rate (koff) at zero force values in the range of ∼10 s(-1). We show that the change in peak rupture force and koff induced by destabilizing the DNA duplex depends on the position of the destabilizing azobenzene photoswitch relative to the force-loading site. When the azobenzenes are proximal to the unzipping end, the decrease in peak force and koff upon azobenzene photoisomerization is significantly larger than when the azobenzene is distal to the site of force loading. We interpret these results as experimental evidence supporting the picture that the destabilization of a double-stranded DNA by a photoswitch isomerization is localized to a small bubble around the photoswitch.
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Affiliation(s)
- Esha Sengupta
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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