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Kretzer B, Herényi L, Csík G, Supala E, Orosz Á, Tordai H, Kiss B, Kellermayer M. TMPyP binding evokes a complex, tunable nanomechanical response in DNA. Nucleic Acids Res 2024:gkae560. [PMID: 38943349 DOI: 10.1093/nar/gkae560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.
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Affiliation(s)
- Balázs Kretzer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Eszter Supala
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Ádám Orosz
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
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Costa EA, Gonçalves AP, Batista JAD, Bazoni RF, Santos AA, Rocha MS. New Insights into the Mechanism of Action of the Drug Chloroquine: Direct Interaction with DNA and Cytotoxicity. J Phys Chem B 2022; 126:3512-3521. [PMID: 35533378 DOI: 10.1021/acs.jpcb.2c01119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloroquine (CLQ) and hydroxychloroquine (HCLQ) are compounds largely employed in the treatment of various human diseases for decades. Nevertheless, a number of intrinsic details concerning their mechanisms of action, especially at the molecular level, are still unknown or have presented controversial results in the literature. Using optical tweezers, here, we investigate at the single-molecule level the molecular mechanism of action of the drug CLQ in its intrinsic interaction with the double-stranded (ds)DNA molecule, one of its targets inside cells, determining the binding modes and the physicochemical (binding) parameters of the interaction. In particular, we show that the ionic strength of the surrounding medium strongly influences such interaction, changing even the main binding mode. In addition, the cytotoxicity of CLQ against three different cell lines was also investigated here, allowing one to evaluate and compare the effect of the drug on the cell viability. In particular, we show that CLQ is highly cytotoxic at a very low (a few micromolar) concentration range for all cell lines tested. These results were rigorously compared to the equivalent ones obtained for the closely related compound hydroxychloroquine (HCLQ), allowing a critical comparison between the action of these drugs at the molecular and cellular levels.
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Affiliation(s)
- Ethe A Costa
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Amanda P Gonçalves
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Josiane A D Batista
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36.036-900, Brazil
| | - Raniella F Bazoni
- Departamento de Ciências Naturais, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo 29.932-900, Brazil
| | - Anésia A Santos
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Márcio S Rocha
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
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Dai J, Zhang H, Huang C, Chen Z, Han A. A Gel-Based Separation-Free Point-of-Care Device for Whole Blood Glucose Detection. Anal Chem 2020; 92:16122-16129. [DOI: 10.1021/acs.analchem.0c03801] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jing Dai
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Han Zhang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Zheyuan Chen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Center for Remote Health Technologies & Systems, Texas A&M University, College Station, Texas 77843 United States
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Prabakaran A, Vijayakumar V, Radhakrishnan N, Chidambaram R, Muthu S. Experimental and Quantum Chemical Computational Analysis of Novel N4,N4′-Dimethyl-[1,1′-Biphenyl]-3,3′,4,4′-Tetraamine. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1756356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Arunachalam Prabakaran
- Department of Physics, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Chennai, Tamil Nadu, India
| | | | - Narayanaswamy Radhakrishnan
- Department of Biochemistry, St. Peter’s Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | | | - Sambanthan Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, Tamil Nadu, India
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5
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Dorfman KD. The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics. J Biomech Eng 2018; 140:2653367. [PMID: 28857114 PMCID: PMC5816256 DOI: 10.1115/1.4037790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/16/2017] [Indexed: 12/28/2022]
Abstract
The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.
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Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and
Materials Science,
University of Minnesota—Twin Cities,
421 Washington Ave SE,
Minneapolis, MN 55455
e-mail:
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Reis LA, Rocha MS. DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes. Biopolymers 2017; 107. [DOI: 10.1002/bip.23015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 01/10/2023]
Affiliation(s)
- L. A. Reis
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
| | - M. S. Rocha
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
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Silva EF, Bazoni RF, Ramos EB, Rocha MS. DNA-doxorubicin interaction: New insights and peculiarities. Biopolymers 2017; 107. [PMID: 27718222 DOI: 10.1002/bip.22998] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/25/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
We have investigated the interaction of the DNA molecule with the anticancer drug doxorubicin (doxo) by using three different experimental techniques: single molecule stretching, single molecule imaging, and dynamic light scattering. Such techniques allowed us to get new insights on the mechanical behavior of the DNA-doxo complexes as well as on the physical chemistry of the interaction. First, the contour length data obtained from single molecule stretching were used to extract the physicochemical parameters of the DNA-doxo interaction under different buffer conditions. This analysis has proven that the physical chemistry of such interaction can be modulated by changing the ionic strength of the surrounding buffer. In particular we have found that at low ionc strengths doxo interacts with DNA by simple intercalation (no aggregation) and/or by forming bound dimers. For high ionic strengths, otherwise, doxo-doxo self-association is enhanced, giving rise to the formation of bound doxo aggregates composed by 3 to 4 molecules along the double-helix. On the other hand, the results obtained for the persistence length of the DNA-doxo complexes is strongly force-dependent, presenting different behaviors when measured with stretching or non-stretching techniques.
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Affiliation(s)
- E F Silva
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R F Bazoni
- 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
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Crisafuli FAP, da Silva LHM, Ferreira GMD, Ramos EB, Rocha MS. Depletion interactions and modulation of DNA-intercalators binding: Opposite behavior of the “neutral” polymer poly(ethylene-glycol). Biopolymers 2016; 105:227-33. [DOI: 10.1002/bip.22789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/17/2015] [Accepted: 11/22/2015] [Indexed: 11/11/2022]
Affiliation(s)
- F. A. P. Crisafuli
- Departamento de Física; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - L. H. M. da Silva
- Departamento de Química; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - G. M. D. Ferreira
- Departamento de Química; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - E. B. Ramos
- Departamento de Física; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - M. S. Rocha
- Departamento de Física; Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
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Doing more with less: fluorescence in situ hybridization and gene sequencing assays can be reliably performed on archival stained tumor tissue sections. Virchows Arch 2016; 468:451-61. [DOI: 10.1007/s00428-016-1906-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/20/2015] [Accepted: 01/13/2016] [Indexed: 12/11/2022]
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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.
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Affiliation(s)
- R F Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa. Viçosa, Minas Gerais, Brazil.
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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.
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Affiliation(s)
- M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
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12
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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]
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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.
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Affiliation(s)
- M S Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa , Viçosa, Minas Gerais, 36570-000, Brazil
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