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Issar U, Arora R, Kakkar R. In silico studies of the interaction of the minor groove binder Hoechst 33258 with B-DNA. J Biomol Struct Dyn 2024; 42:4537-4552. [PMID: 37301606 DOI: 10.1080/07391102.2023.2220807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Interaction of the minor groove binder, Hoechst 33258, with the Dickerson-Drew DNA dodecamer sequence has been investigated using docking, MM/QM, MM/GBSA and molecular dynamics computations to study the modes of binding and the interactions responsible for the binding. Besides the original Hoechst 33258 ligand (HT), a total of 12 ionization and stereochemical states for the ligand are obtained at the physiological pH and have been docked into B-DNA. These states have one or the other or both benzimidazole rings in protonated states, apart from the piperazine nitrogen, which has a quaternary nitrogen in all the states. Most of these states are found to exhibit good docking scores and free energy of binding with B-DNA. The best docked state has been taken further for molecular dynamics simulations and compared with the original HT. This state is protonated at both benzimidazole rings besides the piperazine ring and hence has very highly negative coulombic interaction energy. In both cases, there are strong coulombic interactions, but these are offset by the almost equally unfavorable solvation energies. Thus, the nonpolar forces, particularly van der Waals contacts, dominate the interaction, and the polar interactions highlight subtle changes in the binding energies, leading to more highly protonated states having more negative binding energies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Upasana Issar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Kalindi College, University of Delhi, Delhi, India
| | - Richa Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Shivaji College, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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2
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Valdes-García J, Viviano-Posadas AO, Rivera-Chávez J, Ramírez-Apan T, Martínez-Vargas S, Aguirre-Hernández E, German-Acacio JM, Morales-Morales D, Dorazco-González A. Crystal structures and study of interaction mode of bis-benzimidazole-benzene derivatives with DNA. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131582] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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Yuan X, Tian Y, Liu C, Zhang Z. Environmental factors in Parkinson's disease: New insights into the molecular mechanisms. Toxicol Lett 2021; 356:1-10. [PMID: 34864130 DOI: 10.1016/j.toxlet.2021.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/25/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]
Abstract
Parkinson's disease is a chronic, progressive neurodegenerative disorder affecting 2-3% of the population ≥65 years. It has long been characterized by motor impairment, autonomic dysfunction, and psychological and cognitive changes. The pathological hallmarks are intracellular inclusions containing α-synuclein aggregates and the loss of dopaminergic neurons in the substantia nigra. Parkinson's disease is thought to be caused by a combination of various pathogenic factors, including genetic factors, environmental factors, and lifestyles. Although much research has focused on the genetic causes of PD, environmental risk factors also play a crucial role in the development of the disease. Here, we summarize the environmental risk factors that may increase the occurrence of PD, as well as the underlying molecular mechanisms.
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Affiliation(s)
- Xin Yuan
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ye Tian
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Chaoyang Liu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China; Research Center for Environment and Health, Zhongnan University of Economics and Law, Wuhan, 430073, China
| | - Zhentao Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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4
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Lee C, Kim YJ, Kim KS, Lee JY, Kim DN. Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules. Nucleic Acids Res 2021; 49:12591-12599. [PMID: 34850119 PMCID: PMC8643692 DOI: 10.1093/nar/gkab1119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Kyung Soo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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DNA Dyes-Highly Sensitive Reporters of Cell Quantification: Comparison with Other Cell Quantification Methods. Molecules 2021; 26:molecules26185515. [PMID: 34576986 PMCID: PMC8465179 DOI: 10.3390/molecules26185515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Cell quantification is widely used both in basic and applied research. A typical example of its use is drug discovery research. Presently, plenty of methods for cell quantification are available. In this review, the basic techniques used for cell quantification, with a special emphasis on techniques based on fluorescent DNA dyes, are described. The main aim of this review is to guide readers through the possibilities of cell quantification with various methods and to show the strengths and weaknesses of these methods, especially with respect to their sensitivity, accuracy, and length. As these methods are frequently accompanied by an analysis of cell proliferation and cell viability, some of these approaches are also described.
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6
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Flanagan SP, Fogel R, Edkins AL, Ho LSJ, Limson J. Nonspecific nuclear uptake of anti-MUC1 aptamers by dead cells: the role of cell viability monitoring in aptamer targeting of membrane-bound protein cancer biomarkers. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1191-1203. [PMID: 33605950 DOI: 10.1039/d0ay01878c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Most aptamers targeting cell-expressed antigens are intended for in vivo application, however, these sequences are commonly generated in vitro against synthetic oligopeptide epitopes or recombinant proteins. As these in vitro analogues frequently do not mimic the in vivo target within an endogenous environment, the evolved aptamers are often prone to nonspecific binding. The presence of dead cells and cellular debris further complicate aptamer targeting, due to their high nonspecific affinities to single-stranded DNA. Despite these known limitations, assessment of cell viability and/or the removal of dead cells is rarely applied as part of the methodology during in vivo testing of aptamer binding. Furthermore, the extent and route(s) by which dead cells uptake existing aptamers remains to be determined in the literature. For this purpose, the previously reported aptamer sequences 5TR1, 5TR4, 5TRG2 and S22 - enriched against the MUC1 tumour marker of the mucin glycoprotein family - were used as model sequences to evaluate the influence of cell viability and the presence of nontarget cell-expressed protein on aptamer binding to the MUC1 expressing human cancer cell lines MCF-7, Hs578T, SW480, and SW620. From fluorescence microscopy analysis, all tested aptamers demonstrated extensive nonspecific uptake within the nuclei of dead cells with compromised membrane integrities. Using fluorescent-activated cell sorting (FACS), the inclusion of excess double-stranded DNA as a blocking agent showed no effect on nonspecific aptamer uptake by dead cells. Further nonspecific binding to cell-membrane bound and intracellular protein was evident for each aptamer sequence, as assessed by southwestern blotting and FACS. These factors likely contributed to the ∼120-fold greater binding response of the 5TR1 aptamer to dead MCF-7 cells over equivalent live cell populations. The identification of dead cells and cellular debris using viability stains and the subsequent exclusion of these cells from FACS analysis was identified as an essential requirement for the evaluation of aptamer binding specificity to live cell populations of the cancer cell lines MCF-7, Hs578T and SW480. The research findings stress the importance of dead cell uptake and more comprehensive cell viability screening to validate novel aptamer sequences for diagnostic and therapeutic application.
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Salehi F, Behboudi H, Kavoosi G, Ardestani SK. Incorporation of Zataria multiflora essential oil into chitosan biopolymer nanoparticles: A nanoemulsion based delivery system to improve the in-vitro efficacy, stability and anticancer activity of ZEO against breast cancer cells. Int J Biol Macromol 2020; 143:382-392. [DOI: 10.1016/j.ijbiomac.2019.12.058] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/30/2019] [Accepted: 12/07/2019] [Indexed: 12/23/2022]
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8
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Morozov VN, Kuzmin VA. fluorescence self-quenching of Hoechst 33258 and SYBR Green I Dyes in a DNA Cholesteric liquid-Crystalline matrix. HIGH ENERGY CHEMISTRY 2019. [DOI: 10.1134/s0018143919020103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Guo Z, Xu J, Xia J, Wu Z, Lei J, Yu J. Anti-inflammatory and antitumour activity of various extracts and compounds from the fruits of Piper longum L. ACTA ACUST UNITED AC 2019; 71:1162-1171. [PMID: 31049982 DOI: 10.1111/jphp.13099] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/02/2019] [Accepted: 04/07/2019] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To explore effective extraction method and to find active constituents, we investigated the biological activity of three extracts and isolated active compounds from the fruits of Piper longum L. METHODS Three extracts from the fruits were obtained by reflux, ultrasonic and supercritical fluid extraction, respectively. Active compounds were isolated by the bioassay-guided method. The anti-inflammatory activity, antiproliferation activity and cytotoxicity were evaluated. The apoptosis was detected by Hoechst 33258 staining assay. The relevant proteins were investigated by Western blot assay. KEY FINDINGS The anti-inflammatory activity and cytotoxicity of supercritical fluid extract (SE) were stronger than those of the other two extracts. Among all isolated compounds, the anti-inflammatory activity of eight compounds was stronger than that of indomethacin, and compounds 8, 9, 11, 14 and 15 were found to possess anti-inflammatory effect for the first time. Compounds 1, 2, 3 and 14 exhibited significant cytotoxicity against cancer cells. SE and piperine were found to reduce colony formation, inhibit cell migration and promote apoptosis through increasing cleaved PARP and the ratio of Bax/Bcl-2. CONCLUSIONS The anti-inflammatory and antitumour effects of SE were better than those of the other two extracts. The compounds responsible for the activity were elucidated. SE and piperine inhibit cell growth through apoptosis.
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Affiliation(s)
- Ziyan Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Jie Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Jianhua Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Zi Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | | | - Jianqing Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
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10
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Nascimento FR, Moura TA, Baeta JV, Publio BC, Ferreira PM, Santos AA, França AA, Rocha MS, Diaz-Muñoz G, Diaz MA. New antineoplastic agent based on a dibenzoylmethane derivative: Cytotoxic effect and direct interaction with DNA. Biophys Chem 2018; 239:1-6. [DOI: 10.1016/j.bpc.2018.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/28/2018] [Accepted: 04/28/2018] [Indexed: 11/26/2022]
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11
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Lima CHM, de Paula HMC, da Silva LHM, Rocha MS. Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA). Biopolymers 2017; 107. [DOI: 10.1002/bip.23071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 02/02/2023]
Affiliation(s)
- C. H. M. Lima
- Departamento de Física, Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - H. M. C. de Paula
- Departamento de Química, Universidade Federal de Viçosa; Viçosa Minas Gerais Brazil
| | - L. H. M. da Silva
- Departamento de Química, 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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12
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Issar U, Kumari T, Arora R, Kakkar R. Conformational properties of DNA minor groove binder Hoechst 33258 in gas phase and in aqueous solution. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Rocha JCB, Silva EF, Oliveira MF, Sousa FB, Teixeira AVNC, Rocha MS. β-Cyclodextrin polymer binding to DNA: Modulating the physicochemical parameters. Phys Rev E 2017; 95:052416. [PMID: 28618573 DOI: 10.1103/physreve.95.052416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Indexed: 11/07/2022]
Abstract
Cyclodextrins and cyclodextrins-modified molecules have interesting and appealing properties due to their capacity to host components that are normally insoluble or poorly soluble in water. In this work, we investigate the interaction of a β-cyclodextrin polymer (poly-β-CD) with λ-DNA. The polymers are obtained by the reaction of β-CD with epichlorohydrin in alkaline conditions. We have used optical tweezers to characterize the changes of the mechanical properties of DNA molecules by increasing the concentration of poly-β-CD in the sample. The physical chemistry of the interaction is then deduced from these measurements by using a recently developed quenched-disorder statistical model. It is shown that the contour length of the DNA does not change in the whole range of poly-β-CD concentration (<300μM). On the other hand, significant alterations were observed in the persistence length that identifies two binding modes corresponding to the clustering of ∼2.6 and ∼14 polymer molecules along the DNA double helix, depending on the polymer concentration. Comparing these results with the ones obtained for monomeric β-CD, it was observed that the concentration of CD that alters the DNA persistence length is considerably smaller when in the polymeric form. Also, the binding constant of the polymer-DNA interaction is three orders of magnitude higher than the one found for native (monomeric) β-CD. These results show that the polymerization of the β-CD strongly increases its binding affinity to the DNA molecule. This property can be wisely used to modulate the binding of cyclodextrins to the DNA double helix.
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Affiliation(s)
- J C B Rocha
- Departamento de Física, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.,Instituto Federal do Norte de Minas Gerais-Campus Avançado Janaúba, 39440-000 Janaúba, MG, Brazil
| | - E F Silva
- Departamento de Física, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - M F Oliveira
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - F B Sousa
- Instituto de Física e Química, Universidade Federal de Itajubá, 37500-903 Itajubá, MG, Brazil
| | - A V N C Teixeira
- Departamento de Física, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
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14
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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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15
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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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16
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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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17
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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.
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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
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18
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Abstract
We have investigated the interaction between the native neutral β-cyclodextrin (CD) and the DNA molecule by performing single-molecule stretching experiments with optical tweezers. In particular, we have monitored the changes of the mechanical properties of the CD-DNA complexes as a function of the CD concentration in the sample. By using a quenched disorder statistical model, we were also capable to extract important physicochemical information (equilibrium binding constants, cooperativity degree) of such interaction from the mechanical data. In addition, we have found that the interaction occurs by two different mechanisms, first with the formation of relatively large CD clusters along the double helix, which thereafter can locally denature the DNA molecule by forming hydrogen bonds with the base pairs that eventually flip out. A prediction of our quenched disorder model was that cooperativity could be controlled by adjusting the surface charge of β-CD molecules. This prediction is confirmed in the present work.
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Affiliation(s)
- P S Alves
- Departamento de Física, Universidade Federal de Minas Gerais , Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - O N Mesquita
- Departamento de Física, Universidade Federal de Minas Gerais , Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa , Av. P. H. Rolfs s/n, Viçosa, Minas Gerais 36570-900, Brazil
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19
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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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20
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DAI C, CHEN S, WANG C, ZHANG L, GE K, ZHANG J. Ytterbium ion promotes apoptosis of primary mouse bone marrow stromal cells? J RARE EARTH 2015. [DOI: 10.1016/s1002-0721(14)60439-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Busto N, Cano B, Tejido R, Biver T, Leal JM, Venturini M, Secco F, García B. Aggregation features and fluorescence of Hoechst 33258. J Phys Chem B 2015; 119:4575-81. [PMID: 25759973 DOI: 10.1021/jp512306c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functionality of the bisbenzimide Hoechst 33258 in solution has been largely exploited in the quantification of DNA. Understanding of its behavior is essential to promote its widespread application and learning of biological processes. A detailed study of the dimerization process of the fluorescent blue dye Hoechst 33258 is carried out by isothermal titration calorimetry, absorbance, fluorescence, differential scanning calorimetry and T-jump kinetic measurements. The dimer/monomer ratio depends on the dye concentration and the ionic strength. The dimerization constant determined under physiological conditions (pH = 7.0; I = 0.10 M), KD = 3 × 10(4) M(-1), conveys that only micromolar concentrations of the dye can ensure reasonably high amounts of the monomer species in solution. For instance, for 10 μM dye content, the dimer prevails for I > 0.08 M, whereas the monomer is observed at low ionic strength, a key issue to be elucidated as long as the dimer species is more fluorescent than the monomer and the fluorescence intensity strongly relies on the ionic strength and the dye concentration.
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Affiliation(s)
- Natalia Busto
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Beatriz Cano
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Rocío Tejido
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Tarita Biver
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - José M Leal
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Marcella Venturini
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Fernando Secco
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Begoña García
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
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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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23
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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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24
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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
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