1
|
Bazoni RF, Moura TA, Rocha MS. Hydroxychloroquine Exhibits a Strong Complex Interaction with DNA: Unraveling the Mechanism of Action. J Phys Chem Lett 2020; 11:9528-9534. [PMID: 33115235 DOI: 10.1021/acs.jpclett.0c02590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In the past months, the use of the drug hydroxychloroquine has considerably increased in many countries, associated with a proposed treatment for the COVID-19 disease. Although there is no conclusive evidence about the efficacy of the drug for this purpose, surprisingly there are no conclusive studies in the literature concerning its mechanism of action inside cells, which is related to its interaction with nucleic acids. Here, we performed a robust characterization of the interaction between hydroxychloroquine and double-stranded DNA using single-molecule force spectroscopy and gel electrophoresis. Two different binding modes were identified, namely, minor groove binding for low drug concentrations and intercalation for high drug concentrations, and the sets of binding parameters were determined for each of these modes. Such results have unraveled in detail the molecular mechanism of action of the drug as a DNA ligand.
Collapse
Affiliation(s)
- R F Bazoni
- Departamento de Ciências Naturais, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo 29.932-540, Brazil
| | - T A Moura
- Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais 36.570-900, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais 36.570-900, Brazil
| |
Collapse
|
2
|
Bernal WFP, Silva EF, Rocha MS. Unraveling the physical chemistry and the mixed binding modes of complex DNA ligands by single molecule stretching experiments. RSC Adv 2016. [DOI: 10.1039/c6ra22980h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In this work we present a complete methodology to unravel the physical chemistry and the mixed binding modes of complex DNA ligands.
Collapse
Affiliation(s)
- W. F. P. Bernal
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| | - E. F. Silva
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| | - M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| |
Collapse
|
3
|
Zhou Z, Hu Y, Shan X, Li W, Bai X, Wang P, Lu X. Revealing Three Stages of DNA-Cisplatin Reaction by a Solid-State Nanopore. Sci Rep 2015; 5:11868. [PMID: 26148968 PMCID: PMC4493569 DOI: 10.1038/srep11868] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/09/2015] [Indexed: 12/22/2022] Open
Abstract
The dynamic structural behavior in DNA due to interaction with cisplatin is essential for the functionality of platinum-based anti-cancer drugs. Here we report a novel method to monitor the interaction progress in DNA-cisplatin reaction in real time with a solid-state nanopore. The interaction processes are found to be well elucidated by the evolution of the capture rate of DNA-cisplatin complex, which is defined as the number of their translocation events through the nanopore in unit time. In the first stage, the capture rate decreases rapidly due to DNA discharging as the positive-charged hydrated cisplatin molecules initially bond to the negative-charged DNA and form mono-adducts. In the second stage, by forming di-adducts, the capture rate increases as DNA molecules are softened, appears as the reduced persistence length of the DNA-cisplatin adducts. In the third stage, the capture rate decreases again as a result of DNA aggregation. Our study demonstrates a new single-molecule tool in exploring dynamic behaviors during drug-DNA reactions and may have future application in fast drug screening.
Collapse
Affiliation(s)
- Zhi Zhou
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Ying Hu
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Xinyan Shan
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Wei Li
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Xuedong Bai
- 1] Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China [2] Collaborative Innovation Center of Quantum Matter, Beijing 100190, People's Republic of China
| | - Pengye Wang
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Xinghua Lu
- 1] Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China [2] Collaborative Innovation Center of Quantum Matter, Beijing 100190, People's Republic of China
| |
Collapse
|
4
|
Bazoni RF, Lima CHM, Ramos EB, Rocha MS. Force-dependent persistence length of DNA-intercalator complexes measured in single molecule stretching experiments. SOFT MATTER 2015; 11:4306-4314. [PMID: 25913936 DOI: 10.1039/c5sm00706b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
By using optical tweezers with an adjustable trap stiffness, we have performed systematic single molecule stretching experiments with two types of DNA-intercalator complexes, in order to investigate the effects of the maximum applied forces on the mechanical response of such complexes. We have explicitly shown that even in the low-force entropic regime the persistence length of the DNA-intercalator complexes is strongly force-dependent, although such behavior is not exhibited by bare DNA molecules. We discuss the possible physicochemical effects that can lead to such results. In particular, we propose that the stretching force can promote partial denaturation on the highly distorted double-helix of the DNA-intercalator complexes, which interfere strongly in the measured values of the persistence length.
Collapse
Affiliation(s)
- R F Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais, Brazil.
| | | | | | | |
Collapse
|
5
|
Rocha MS. Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments. Integr Biol (Camb) 2015; 7:967-86. [DOI: 10.1039/c5ib00127g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review we focus on the idea of establishing connections between the mechanical properties of DNA–ligand complexes and the physical chemistry of DNA–ligand interactions.
Collapse
Affiliation(s)
- M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| |
Collapse
|
6
|
Characterizing the interaction between DNA and GelRed fluorescent stain. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 44:1-7. [DOI: 10.1007/s00249-014-0995-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/13/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
|
7
|
Rocha MS, Cavalcante AG, Silva R, Ramos EB. On the effects of intercalators in DNA condensation: a force spectroscopy and gel electrophoresis study. J Phys Chem B 2014; 118:4832-9. [PMID: 24720756 DOI: 10.1021/jp501589d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work we have characterized the effects of the intercalator ethidium bromide (EtBr) on the DNA condensation process by using force spectroscopy and gel electrophoresis. We have tested two condensing agents: spermine (spm(4+)), a tetravalent cationic amine which promotes cation-induced DNA condensation, and poly(ethylene glycol) (PEG), a neutral polymer which promotes DNA ψ-condensation. Two different types of experiments were performed. In the first type, bare DNA molecules disperse in solution are first treated with EtBr for intercalation, and then the condensing agent is added to the sample with the purpose of verifying the effects of the intercalator in hindering DNA condensation. In the second experiment type, the bare DNA molecules are first condensed, and then the intercalator is added to the sample in order to verify its influence on the previously condensed DNA. The results obtained with the two different experimental techniques used agree very well, indicating that previously intercalated EtBr can hinder both cation-induced and ψ-condensation, being more efficient in the first case. On the other hand, EtBr has little effect on the previously formed cation-induced condensates, but is efficient in unfolding the ψ-condensates.
Collapse
Affiliation(s)
- M S Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa , Viçosa, Minas Gerais, 36570-000, Brazil
| | | | | | | |
Collapse
|
8
|
Reis LA, Ramos EB, Rocha MS. DNA Interaction with Diaminobenzidine Studied with Optical Tweezers and Dynamic Light Scattering. J Phys Chem B 2013; 117:14345-50. [DOI: 10.1021/jp409544e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. A. Reis
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E. B. Ramos
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M. S. Rocha
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
9
|
Doughty B, Rao Y, Kazer SW, Kwok SJJ, Turro NJ, Eisenthal KB. Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation. J Phys Chem B 2013; 117:15285-9. [DOI: 10.1021/jp311634a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Benjamin Doughty
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Yi Rao
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Samuel W. Kazer
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Sheldon J. J. Kwok
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Nicholas J. Turro
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Kenneth B. Eisenthal
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| |
Collapse
|
10
|
Cesconetto EC, Junior FSA, Crisafuli FAP, Mesquita ON, Ramos EB, Rocha MS. DNA interaction with Actinomycin D: mechanical measurements reveal the details of the binding data. Phys Chem Chem Phys 2013; 15:11070-7. [DOI: 10.1039/c3cp50898f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Kostjukov VV, Evstigneev MP. Relation between the change in DNA elasticity on ligand binding and the binding energetics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:031919. [PMID: 23030956 DOI: 10.1103/physreve.86.031919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 06/28/2012] [Indexed: 06/01/2023]
Abstract
The widespread use of tweezers for measurement of ligand-DNA binding parameters is based on the McGhee-von Hippel treatment of the DNA contour and persistence length as a function of concentration. The McGhee-von Hippel approach contains the basic assumption that the binding constant K is independent of the number of already bound ligands. However, the change in elasticity of DNA on binding affects the entropic part of the Gibbs free energy and, hence, the K value in a concentration-dependent manner, making the whole approach inconsistent. In the present work we show that the energetic effect of DNA stiffening on noncovalent binding of small ligands is negligible with respect to the net energy of reaction, whereas the DNA stiffening on binding of large ligands must always be considered in each particular case.
Collapse
Affiliation(s)
- Viktor V Kostjukov
- Department of Physics, Sevastopol National Technical University, Universitetskaya street 33, Sevastopol, 99053, Ukraine
| | | |
Collapse
|
12
|
Crisafuli FAP, Cesconetto EC, Ramos EB, Rocha MS. DNA–cisplatin interaction studied with single molecule stretching experiments. Integr Biol (Camb) 2012; 4:568-74. [DOI: 10.1039/c2ib00183g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- F. A. P. Crisafuli
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, MG, Brazil, Fax: +55 31 3899 2483; Tel: +55 31 3899 3399
| | - E. C. Cesconetto
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, MG, Brazil, Fax: +55 31 3899 2483; Tel: +55 31 3899 3399
| | - E. B. Ramos
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, MG, Brazil, Fax: +55 31 3899 2483; Tel: +55 31 3899 3399
| | - M. S. Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, MG, Brazil, Fax: +55 31 3899 2483; Tel: +55 31 3899 3399
| |
Collapse
|
13
|
Celedon A, Wirtz D, Sun S. Torsional mechanics of DNA are regulated by small-molecule intercalation. J Phys Chem B 2010; 114:16929-35. [PMID: 21090816 DOI: 10.1021/jp107541q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Whether the bend and twist mechanics of DNA molecules are coupled is unclear. Here, we report the direct measurement of the resistive torque of single DNA molecules to study the effect of ethidium bromide (EtBr) intercalation and pulling force on DNA twist mechanics. DNA molecules were overwound and unwound using recently developed magnetic tweezers where the molecular resistive torque was obtained from Brownian angular fluctuations. The effect of EtBr intercalation on the twist stiffness was found to be significantly different from the effect on the bend persistence length. The twist stiffness of DNA was dramatically reduced at low intercalator concentration (<10 nM); however, it did not decrease further when the intercalator concentration was increased by 3 orders of magnitude. We also determined the dependence of EtBr intercalation on the torque applied to DNA. We propose a model for the elasticity of DNA base pairs with intercalated EtBr molecules to explain the abrupt decrease of twist stiffness at low EtBr concentration. These results indicate that the bend and twist stiffnesses of DNA are independent and can be differently affected by small-molecule binding.
Collapse
Affiliation(s)
- Alfredo Celedon
- Johns Hopkins Physical Science Oncology Center, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
| | | | | |
Collapse
|
14
|
|