1
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Kodipaka A, Vuradi RK, Airva PK, Nambigari N, Sirasani S. Application of Novel Ruthenium (II) Polypyridyl Complexes as Robust DNA Probes, Optical Material and Antimicrobials-An Experimental and DFT Approach. J Fluoresc 2024:10.1007/s10895-024-03626-8. [PMID: 38602589 DOI: 10.1007/s10895-024-03626-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/19/2024] [Indexed: 04/12/2024]
Abstract
The nature of the interaction of DNA with heteroleptic Ruthenium (II) Polypyridyl complexes of the type [Ru (A)2TPIP]2+, where TPIP = 2-(1-p-tolyl-1H pyrazol-4 -yl)-1H-imidazo [4, 5-f[1. 10] phenanthroline and A = 1,10 phenanthroline (1),4,4'-dimethyl-1,10-ortho Phenanthroline (2), 2,2' - bipyridine (3) and 4, 4' dimethyl 2, 2'- bipyridine (4), has been investigated by experimentaland molecular docking approaches. The order of the DNA binding affinities of the synthesised complexes is 1 > 2 > 3 > 4. The findings imply that the unsubstituted complex has a better affinity to bind with DNA than the substituted (dmp and dmb) emphasizing the significance of the auxiliary ligand. Additionally, as the medium's ionic strength drops, the DNA/Ru ratio rises, or when water is displaced by glycerol, the intercalation of complexes into DNA increases. DFT calculations at the B3LYP/LANL2MB level was used for molecular geometry (Ground State) and electronic characteristic calculations. The HOMO-LUMO gap of the Ru [II] complex is less than the intercalator and hence kinetically labile. Among the complexes, the bpy complex has shown utmost non-linear optical properties (α = -153.9099 10-24esu and β = 3.8498 10-30esu). The docking study shows the significance of the Metal-intercalator's shorter length may increase DNA binding affinity. This study divulges that the Ruthenium (II) polypyridyl complexes bind to DNA preponderantly by intercalation supporting Viscosity studies. All the complexes have a considerable attraction for guanine. The standard disk diffusion method reveals that complexes (1, 2, 3 and 4) have good antibacterial activity.
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Affiliation(s)
- Aruna Kodipaka
- Department of Chemistry, University College of Science, Osmania University, Saifabad, Hyderabad, 500 004, Telangana, India
| | - Ravi Kumar Vuradi
- Department of Chemistry, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Praveen Kumar Airva
- Department of Biotechnology, Sri Satya Sai University of Technology & Medical Sciences, Bhopal- Indore Road, Opp. Oilfed Plant, Sehore, 466001, Madhya Pradesh, India
| | - Navaneetha Nambigari
- Department of Chemistry, University College of Science, Osmania University, Saifabad, Hyderabad, 500 004, Telangana, India.
- Department of Chemistry, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India.
| | - Satyanarayana Sirasani
- Department of Chemistry, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India.
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2
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Göktürk T, Sakallı Çetin E, Hökelek T, Pekel H, Şensoy Ö, Aksu EN, Güp R. Synthesis, Structural Investigations, DNA/BSA Interactions, Molecular Docking Studies, and Anticancer Activity of a New 1,4-Disubstituted 1,2,3-Triazole Derivative. ACS OMEGA 2023; 8:31839-31856. [PMID: 37692230 PMCID: PMC10483525 DOI: 10.1021/acsomega.3c03355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023]
Abstract
We report herein a new 1,2,3-triazole derivative, namely, 4-((1-(3,4-dichlorophenyl)-1H-1,2,3-triazol-4-yl)methoxy)-2-hydroxybenzaldehyde, which was synthesized by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The structure of the compound was analyzed using Fourier transform infrared spectroscopy (FTIR), 1H NMR, 13C NMR, UV-vis, and elemental analyses. Moreover, X-ray crystallography studies demonstrated that the compound adapted a monoclinic crystal system with the P21/c space group. The dominant interactions formed in the crystal packing were found to be hydrogen bonding and van der Waals interactions according to Hirshfeld surface (HS) analysis. The volume of the crystal voids and the percentage of free spaces in the unit cell were calculated as 152.10 Å3 and 9.80%, respectively. The evaluation of energy frameworks showed that stabilization of the compound was dominated by dispersion energy contributions. Both in vitro and in silico investigations on the DNA/bovine serum albumin (BSA) binding activity of the compound showed that the CT-DNA binding activity of the compound was mediated via intercalation and BSA binding activity was mediated via both polar and hydrophobic interactions. The anticancer activity of the compound was also tested by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay using human cell lines including MDA-MB-231, LNCaP, Caco-2, and HEK-293. The compound exhibited more cytotoxic activity than cisplatin and etoposide on Caco-2 cancer cell lines with an IC50 value of 16.63 ± 0.27 μM after 48 h. Annexin V suggests the induction of cell death by apoptosis. Compound 3 significantly increased the loss of mitochondrial membrane potential (MMP) levels in Caco-2 cells, and the reactive oxygen species (ROS) assay proved that compound 3 could induce apoptosis by ROS generation.
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Affiliation(s)
- Tolga Göktürk
- Department
of Chemistry, Muğla Sıtkı
Koçman University, 48000 Muğla, Türkiye
| | - Esin Sakallı Çetin
- Department
of Medical Biology, Muğla Sıtkı
Koçman University, 48000 Muğla, Türkiye
| | - Tuncer Hökelek
- Department
of Physics, Hacettepe University, 06800 Ankara, Türkiye
| | - Hanife Pekel
- Department
of Pharmacy Services, Vocational School of Health Services, Istanbul Medipol University, 34810 Istanbul, Türkiye
| | - Özge Şensoy
- Department
of Computer Engineering, Istanbul Medipol
University, 34000 Istanbul, Türkiye
| | - Ebru Nur Aksu
- Department
of Medical Biology, Muğla Sıtkı
Koçman University, 48000 Muğla, Türkiye
| | - Ramazan Güp
- Department
of Chemistry, Muğla Sıtkı
Koçman University, 48000 Muğla, Türkiye
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3
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Ma J, Huang G, Mo C, Li J, Yan L, Zhang Q. Insights into the intercalative binding of benzo[b]fluoranthene with herring sperm DNA in vitro and its application. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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4
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Liu Y, Pei Y, Xu J, Cheng Y, Tong Q, You H. Force-Dependent Intercalative Bulky DNA Adduct Formation Detected by Single-Molecule Stretching. Anal Chem 2022; 94:13623-13630. [PMID: 36129494 DOI: 10.1021/acs.analchem.2c03594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitatively analyzing the binding topology and reactivity is essential for understanding the cytotoxic or tumorigenic activities of bulky DNA adducts formed by chemotherapeutic drugs or carcinogens. Biochemical methods require purification of DNA and discontinuous steps to digest or label the adducts and thus have difficulties in identifying the binding topology and are not suitable for detecting unstable adducts. Herein, we used a single-molecule stretching assay to characterize the number of intercalative adducts, the formation kinetics, and the mechanical properties of intercalative DNA adducts based on measuring adduct-induced DNA elongation. We analyzed various reactive conditions, including formaldehyde-mediated anthracycline-DNA adducts, UV light-catalyzed psoralen-DNA adducts, and liver S9 fraction-catalyzed aflatoxin B1-DNA adducts. We showed that adduct formation abilities are correlated with the noncovalent intercalation binding ability. External forces on double-stranded DNA increased the intercalation of ligands and can result in a 1.8- to 5.3-fold increase in DNA adduct formation.
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Affiliation(s)
- Yajun Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yufeng Pei
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingjing Xu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Department of Pharmacy, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430077, China
| | - Yuanlei Cheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qingyi Tong
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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5
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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: 1] [Impact Index Per Article: 0.5] [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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6
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Luo H, Liang Y, Zhang H, Liu Y, Xiao Q, Huang S. Comparison on binding interactions of quercetin and its metal complexes with calf thymus DNA by spectroscopic techniques and viscosity measurement. J Mol Recognit 2021; 34:e2933. [PMID: 34432328 DOI: 10.1002/jmr.2933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/08/2022]
Abstract
Quercetin (Qu) and its metal complexes have received great attention during the last years, due to their good antioxidant, antibacterial, and anticancer activities. In this contribution, binding interactions of Qu and Qu-metal complexes with calf thymus DNA (ctDNA) were investigated and compared systematically by using spectroscopic techniques and viscosity measurement. UV-vis absorption spectra of ctDNA-compound systems showed obvious hypochromic effect. Relative viscosity and melting temperature of ctDNA increased after the addition of Qu and Qu-metal complexes, and the change tendency is Qu-Cr(III) > Qu-Mn(II) > Qu-Zn(II) > Qu-Cu(II) > Qu. Fluorescence competition experiments show that hydrogen bonds and van der Waals interaction play an important role in the intercalative binding of Qu and Qu-metal complexes with ctDNA. Qu and Qu-metal complexes could unwind the right-handed B-form helicity of ctDNA and further affect its base pair stacking. Space steric hindrance might be responsible for the differences in the intercalative binding between ctDNA and different Qu-metal complexes. These results provide new information for the molecular understanding of binding interactions of Qu-metal complexes with DNA and the strategy for research of structural influences.
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Affiliation(s)
- Huajian Luo
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Yu Liang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Huiying Zhang
- College of Chemistry and Biological Engineering, Hechi University, Hechi, China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China.,State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry and Chemical Engineering, Tiangong University, Tianjin, China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
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7
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Kim YJ, Park J, Lee JY, Kim DN. Programming ultrasensitive threshold response through chemomechanical instability. Nat Commun 2021; 12:5177. [PMID: 34462430 PMCID: PMC8405678 DOI: 10.1038/s41467-021-25406-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 08/03/2021] [Indexed: 11/09/2022] Open
Abstract
The ultrasensitive threshold response is ubiquitous in biochemical systems. In contrast, achieving ultrasensitivity in synthetic molecular structures in a controllable way is challenging. Here, we propose a chemomechanical approach inspired by Michell's instability to realize it. A sudden reconfiguration of topologically constrained rings results when the torsional stress inside reaches a critical value. We use DNA origami to construct molecular rings and then DNA intercalators to induce torsional stress. Michell's instability is achieved successfully when the critical concentration of intercalators is applied. Both the critical point and sensitivity of this ultrasensitive threshold reconfiguration can be controlled by rationally designing the cross-sectional shape and mechanical properties of DNA rings.
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Affiliation(s)
- Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Junho Park
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Jae Young Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea. .,Department of Mechanical Engineering, Seoul National University, Seoul, Korea. .,Institute of Engineering Research, Seoul National University, Seoul, Korea.
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8
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Mahmud KM, Niloy MS, Shakil MS, Islam MA. Ruthenium Complexes: An Alternative to Platinum Drugs in Colorectal Cancer Treatment. Pharmaceutics 2021; 13:1295. [PMID: 34452256 PMCID: PMC8398452 DOI: 10.3390/pharmaceutics13081295] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the intimidating causes of death around the world. CRC originated from mutations of tumor suppressor genes, proto-oncogenes and DNA repair genes. Though platinum (Pt)-based anticancer drugs have been widely used in the treatment of cancer, their toxicity and CRC cells' resistance to Pt drugs has piqued interest in the search for alternative metal-based drugs. Ruthenium (Ru)-based compounds displayed promising anticancer activity due to their unique chemical properties. Ru-complexes are reported to exert their anticancer activities in CRC cells by regulating different cell signaling pathways that are either directly or indirectly associated with cell growth, division, proliferation, and migration. Additionally, some Ru-based drug candidates showed higher potency compared to commercially available Pt-based anticancer drugs in CRC cell line models. Meanwhile Ru nanoparticles coupled with photosensitizers or anticancer agents have also shown theranostic potential towards CRC. Ru-nanoformulations improve drug efficacy, targeted drug delivery, immune activation, and biocompatibility, and therefore may be capable of overcoming some of the existing chemotherapeutic limitations. Among the potential Ru-based compounds, only Ru (III)-based drug NKP-1339 has undergone phase-Ib clinical trials in CRC treatment.
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Affiliation(s)
- Kazi Mustafa Mahmud
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (K.M.M.); (M.S.N.)
| | - Mahruba Sultana Niloy
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (K.M.M.); (M.S.N.)
| | - Md Salman Shakil
- Department of Pharmacology & Toxicology, University of Otago, Dunedin 9016, New Zealand
- Department of Biochemistry, Primeasia University, Banani, Dhaka 1213, Bangladesh
| | - Md Asiful Islam
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
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9
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Moura TA, Junior RLR, Rocha MS. Caffeine modulates the intercalation of drugs on DNA: A study at the single molecule level. Biophys Chem 2021; 277:106653. [PMID: 34217911 DOI: 10.1016/j.bpc.2021.106653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/15/2021] [Accepted: 06/24/2021] [Indexed: 11/20/2022]
Abstract
We use optical tweezers to characterize the ability of Caffeine (Caf) to modulate the intercalation of drugs into the DNA double-helix at the single molecule level. When previously bound to the double-helix, Caf hinders ethidium bromide (EtBr) intercalation, decreasing its effective equilibrium binding constant with DNA. The dominant mechanism of such singular ability is a direct binding of Caf to the intercalating drugs in solution, which decreases the effective concentration of such compounds available to interact with DNA. When EtBr intercalation into the DNA double-helix occurs firstly, on the other hand, the measured cooperativity between Caf molecules interacting with DNA can be modulated, a feature also correlated to the Caf-EtBr interaction in solution. The results achieved here unveil many peculiarities about the details of such interactions at the molecular level and provide new insights on the use of Caf in therapeutic applications.
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Affiliation(s)
- T A Moura
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R L R Junior
- 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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10
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Huang S, Luo H, Liu Y, Su W, Xiao Q. Comparable investigation of binding interactions between three arene ruthenium(II) thiosemicarbazone complexes and calf thymus DNA. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Tibbs J, Tabei SMA, Kidd TE, Peters JP. Effects of Intercalating Molecules on the Polymer Properties of DNA. J Phys Chem B 2020; 124:8572-8582. [PMID: 32941733 DOI: 10.1021/acs.jpcb.0c06867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomic force microscopy (AFM) enables determination of physical properties from single DNA molecules. Insertion of aromatic molecules into the structure of DNA results in morphological changes. However, the accompanying changes to elastic properties due to this insertion are not fully understood. AFM was used to examine the morphological effects of intercalator binding and report changes in the elastic properties of intrinsically straight DNA molecules. The persistence length and polymer extension were characterized in the presence of three intercalating molecules: ethidium bromide and the less well studied chloroquine and acridine. It was found that all three intercalators significantly increased the bending persistence length. In addition, an analysis of the normal bending modes of the static molecules corroborated these results. This approach of measuring binding effects of intercalators on DNA physical properties using a model system of intrinsically straight DNA is applicable to other DNA binding ligands and other modes of DNA interaction.
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Affiliation(s)
| | | | | | - Justin P Peters
- Department of Chemistry and Biochemistry, University of Northern Iowa 1227 West 27th Street Cedar Falls, Iowa 50614-0423, United States
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12
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Comparable investigation of in vitro interactions between three ruthenium(II) arene complexes with curcumin analogs and ctDNA. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Martínez MÁ, Carranza MP, Massaguer A, Santos L, Organero JA, Aliende C, de Llorens R, Ng-Choi I, Feliu L, Planas M, Rodríguez AM, Manzano BR, Espino G, Jalón FA. Synthesis and Biological Evaluation of Ru(II) and Pt(II) Complexes Bearing Carboxyl Groups as Potential Anticancer Targeted Drugs. Inorg Chem 2017; 56:13679-13696. [DOI: 10.1021/acs.inorgchem.7b01178] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- M Ángeles Martínez
- Department of Chemistry, University of Girona,
Campus Montilivi, 17003 Girona, Catalunya, Spain
- Department
of Biology, University of Girona, Campus Montilivi, 17003 Girona, Catalunya, Spain
| | - M. Pilar Carranza
- Universidad de Castilla-La Mancha, Facultad de Ciencias y Tecnologías Químicas-IRICA, Avda. Camilo J. Cela 10, 13071 Ciudad Real, Spain
| | - Anna Massaguer
- Department
of Biology, University of Girona, Campus Montilivi, 17003 Girona, Catalunya, Spain
| | - Lucia Santos
- Universidad de Castilla-La Mancha, Departamento de Química Física, Avda. Camilo J. Cela s/n, 13071 Ciudad Real, Spain
| | - Juan A. Organero
- Universidad de Castilla-La Mancha, Departamento
de Química Física, Facultad de Ciencias Ambientales
y Bioquímica, and INAMOL, Avenida Carlos III, S.N., 45071 Toledo, Spain
| | - Cristina Aliende
- Universidad de Burgos. Dpto de Química, Facultad de Ciencias, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Rafael de Llorens
- Department
of Biology, University of Girona, Campus Montilivi, 17003 Girona, Catalunya, Spain
| | - Iteng Ng-Choi
- Laboratori d’Innovació en Processos i Productes
de Síntesi Orgànica (LIPPSO), Department of Chemistry, University of Girona,
Campus Montilivi, 17003 Girona, Catalunya, Spain
| | - Lidia Feliu
- Laboratori d’Innovació en Processos i Productes
de Síntesi Orgànica (LIPPSO), Department of Chemistry, University of Girona,
Campus Montilivi, 17003 Girona, Catalunya, Spain
| | - Marta Planas
- Laboratori d’Innovació en Processos i Productes
de Síntesi Orgànica (LIPPSO), Department of Chemistry, University of Girona,
Campus Montilivi, 17003 Girona, Catalunya, Spain
| | - Ana M. Rodríguez
- Universidad de Castilla-La Mancha, Escuela Técnica Superior de
Ingenieros Industriales, Avda. Camilo J. Cela, 13071 Ciudad Real, Spain
| | - Blanca R. Manzano
- Universidad de Castilla-La Mancha, Facultad de Ciencias y Tecnologías Químicas-IRICA, Avda. Camilo J. Cela 10, 13071 Ciudad Real, Spain
| | - Gustavo Espino
- Universidad de Burgos. Dpto de Química, Facultad de Ciencias, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Félix A. Jalón
- Universidad de Castilla-La Mancha, Facultad de Ciencias y Tecnologías Químicas-IRICA, Avda. Camilo J. Cela 10, 13071 Ciudad Real, Spain
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14
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Zadegan RM, Lindau EG, Klein WP, Green C, Graugnard E, Yurke B, Kuang W, Hughes WL. Twisting of DNA Origami from Intercalators. Sci Rep 2017; 7:7382. [PMID: 28785065 PMCID: PMC5547094 DOI: 10.1038/s41598-017-07796-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023] Open
Abstract
DNA nanostructures represent the confluence of materials science, computer science, biology, and engineering. As functional assemblies, they are capable of performing mechanical and chemical work. In this study, we demonstrate global twisting of DNA nanorails made from two DNA origami six-helix bundles. Twisting was controlled using ethidium bromide or SYBR Green I as model intercalators. Our findings demonstrate that DNA nanorails: (i) twist when subjected to intercalators and the amount of twisting is concentration dependent, and (ii) twisting saturates at elevated concentrations. This study provides insight into how complex DNA structures undergo conformational changes when exposed to intercalators and may be of relevance when exploring how intercalating drugs interact with condensed biological structures such as chromatin and chromosomes, as well as chromatin analogous gene expression devices.
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Affiliation(s)
- Reza M Zadegan
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Elias G Lindau
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - William P Klein
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Christopher Green
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Bernard Yurke
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Wan Kuang
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - William L Hughes
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States.
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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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Zou Y, Biao L, Xu F, Liu R, Liu Z, Fu Y. Structural study on the interactions of oxaliplatin and linear DNA. SCANNING 2016; 38:880-888. [PMID: 27391259 DOI: 10.1002/sca.21337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Damage to cellular DNA is believed to determine the cytotoxicity of oxaliplatin. However, high resolution structures formed by oxaliplatin and different linear DNA remain unclear. This study characterized, the key structures of different linear DNA in the platination process by UV absorption spectra and atomic force microscopy (AFM). Bathochromic shift and hyperchromicity in UV spectra after addition of oxaliplatin revealed that it can disrupt base stacking of DNA in the platination process. AFM results of different linear DNA indicated that, the platination process can induce DNA change from an extended conformation to the network structure with many kinks and finally to the compact particles, or toroids with increasing the incubation time. All AFM results confirmed that, platination of different linear DNA by oxaliplatin is a time depended process. The present AFM results provide, structural evidence about the interactions between oxaliplatin and different linear DNA containing multiple targets. SCANNING 38:880-888, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yongpeng Zou
- Department of Cardiology, 2nd Affiliated Hospital of Harbin Medical University, Harbin, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, People's Republic of China
| | - Linhai Biao
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, People's Republic of China
- State Engineering Laboratory of Bio-Resource Eco-Utilization, Northeast Forestry University, Harbin, People's Republic of China
| | - Fengjie Xu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, People's Republic of China
- State Engineering Laboratory of Bio-Resource Eco-Utilization, Northeast Forestry University, Harbin, People's Republic of China
| | - Ruisi Liu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, People's Republic of China
- State Engineering Laboratory of Bio-Resource Eco-Utilization, Northeast Forestry University, Harbin, People's Republic of China
| | - Zhiguo Liu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, People's Republic of China
- State Engineering Laboratory of Bio-Resource Eco-Utilization, Northeast Forestry University, Harbin, People's Republic of China
| | - Yujie Fu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, People's Republic of China
- State Engineering Laboratory of Bio-Resource Eco-Utilization, Northeast Forestry University, Harbin, People's Republic of China
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17
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Banerjee T, Banerjee S, Sett S, Ghosh S, Rakshit T, Mukhopadhyay R. Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy. PLoS One 2016; 11:e0154666. [PMID: 27183010 PMCID: PMC4868319 DOI: 10.1371/journal.pone.0154666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/18/2016] [Indexed: 11/24/2022] Open
Abstract
DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.
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Affiliation(s)
- T. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Banerjee
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Sett
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - S. Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - T. Rakshit
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
| | - R. Mukhopadhyay
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, 700 032, India
- * E-mail:
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18
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Almaqwashi AA, Paramanathan T, Rouzina I, Williams MC. Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy. Nucleic Acids Res 2016; 44:3971-88. [PMID: 27085806 PMCID: PMC4872107 DOI: 10.1093/nar/gkw237] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | | | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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19
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Huang S, Liang Y, Huang C, Su W, Lei X, Liu Y, Xiao Q. Systematical investigation of binding interaction between novel ruthenium(II) arene complex with curcumin analogs and ctDNA. LUMINESCENCE 2016; 31:1384-1394. [DOI: 10.1002/bio.3119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/17/2016] [Accepted: 01/24/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Shan Huang
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
| | - Yu Liang
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
| | - Chusheng Huang
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
| | - Wei Su
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
| | - Xiaolin Lei
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
| | - Yi Liu
- State Key Laboratory of Virology; Wuhan University; Wuhan 430072 People's Republic of China
| | - Qi Xiao
- College of Chemistry and Material Science; Guangxi Teachers Education University; Nanning 530001 People's Republic of China
- Collaborative Innovation Center of Southwest Ethnic Medicine; Guangxi Normal University; Guilin 541004 People's Republic of China
- State Key Laboratory of Virology; Wuhan University; Wuhan 430072 People's Republic of China
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20
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Cassina V, Manghi M, Salerno D, Tempestini A, Iadarola V, Nardo L, Brioschi S, Mantegazza F. Effects of cytosine methylation on DNA morphology: An atomic force microscopy study. Biochim Biophys Acta Gen Subj 2016; 1860:1-7. [DOI: 10.1016/j.bbagen.2015.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/11/2015] [Accepted: 10/08/2015] [Indexed: 12/19/2022]
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21
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Spectroscopic, Electrochemical, andIn SilicoCharacterization of Complex Formed between 2-Ferrocenylbenzoic Acid and DNA. J CHEM-NY 2016. [DOI: 10.1155/2016/7468951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present the synthesis of 2-ferrocenylbenzoic acid (FcOH) and its electrochemical and spectroscopic characterization. FcOH was characterized for interaction with DNA using theoretical and experimental methods. UV-visible spectroscopy and cyclic voltammeter (CV) were used for the experimental account of FcOH-DNA complex. The experimental results showed that the FcOH interacts by electrostatic mode. The binding constant (Kb) and Gibbs free energy (ΔG) for the FcOH-DNA complex have been estimated as 5.3 × 104 M−1and −6.44 kcal/mol, respectively. The theoretical DNA binding of FcOH was studied with AutoDock molecular docking software. The docking studies yield good approximation with experimental data and explain the sites of binding.
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22
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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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23
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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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24
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The fluorescence properties and binding mechanism of SYTOX green, a bright, low photo-damage DNA intercalating agent. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:337-48. [PMID: 26024786 DOI: 10.1007/s00249-015-1027-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
DNA intercalators are widely used in cancer therapeutics, to probe protein-DNA interactions and to investigate the statistical-mechanical properties of DNA. Here, we employ single-molecule fluorescence microscopy, magnetic tweezers, and ensemble-binding assays to investigate the fluorescence properties and binding mechanism of SYTOX green, a DNA labeling dye previously used for staining dead cells and becoming of common use for single-molecule methodologies. Specifically, we show that SYTOX green presents several advantages with respect to other dyes: (1) binds DNA rapidly and with high affinity; (2) has a good signal-to-noise ratio even at low concentrations; (3) exhibits a low photobleaching rate; and (4) induces lower light-induced DNA degradation. Finally, we show that SYTOX green is a DNA intercalator that binds DNA cooperatively with a binding site of 3.5 bp, increasing the DNA length upon binding by 43%, while not affecting its mechanical properties.
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25
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Pal S, Zhang Y, Kumar SK, Gang O. Dynamic tuning of DNA-nanoparticle superlattices by molecular intercalation of double helix. J Am Chem Soc 2015; 137:4030-3. [PMID: 25751093 DOI: 10.1021/ja512799d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanoparticle (NP) assembly using DNA recognition has emerged as a powerful tool for the fabrication of 3D superlattices. In addition to the vast structural diversity, this approach provides an avenue for dynamic 3D NP assembly, which is promising for the modulation of interparticle distances and, hence, for example, for in situ tuning of optical properties. While several approaches have been explored for changing NP separations in the lattices using responsiveness of single-stranded DNA (ss-DNA), far less work has been done for the manipulation of most abundant double-stranded DNA (ds-DNA) motifs. Here, we present a novel strategy for modulation of interparticle distances in DNA linked 3D self-assembled NP lattices by molecular intercalator. We utilize ethidium bromide (EtBr) as a model intercalator to demonstrate selective and isotropic lattice expansion for three superlattice types (bcc, fcc, and AlB2) due to the intercalation of ds-DNA linking NPs. We further show the reversibility of the lattice parameter using n-butanol as a retrieving agent as well as an increased lattice thermal stability by 12-14 °C due to the inclusion of EtBr. The proposed intercalator-based strategy permits the creation of reconfigurable and thermally stable superlattices, which could lead to tunable and functionally responsive materials.
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Affiliation(s)
- Suchetan Pal
- †Department of Chemical Engineering, Columbia University, New York City, New York 10027, United States.,‡Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yugang Zhang
- ‡Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Sanat K Kumar
- †Department of Chemical Engineering, Columbia University, New York City, New York 10027, United States
| | - Oleg Gang
- ‡Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
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26
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Sato S, Umeda Y, Fujii S, Takenaka S. Cooperative Binding of Ferrocenylnaphthalene Diimide Carrying β-Cyclodextrin Converts Double-Stranded DNA to a Rod-Like Structure. Bioconjug Chem 2015; 26:379-82. [DOI: 10.1021/bc500535n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Shinobu Sato
- Department of Applied Chemistry, ‡Research Center
for Biomicrosensing Technology, and §Department of
Bioscience and Bioinformatics, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu, Fukuoka 804-8550, Japan
| | - Yuta Umeda
- Department of Applied Chemistry, ‡Research Center
for Biomicrosensing Technology, and §Department of
Bioscience and Bioinformatics, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu, Fukuoka 804-8550, Japan
| | - Satoshi Fujii
- Department of Applied Chemistry, ‡Research Center
for Biomicrosensing Technology, and §Department of
Bioscience and Bioinformatics, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu, Fukuoka 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, ‡Research Center
for Biomicrosensing Technology, and §Department of
Bioscience and Bioinformatics, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu, Fukuoka 804-8550, Japan
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27
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Huang S, Zhu F, Xiao Q, Liang Y, Zhou Q, Su W. Thermodynamic investigation of the interaction between the [(η6-p-cymene)Ru(benzaldehyde-N4-phenylthiosemicarbazone)Cl]Cl anticancer drug and ctDNA: multispectroscopic and electrochemical studies. RSC Adv 2015. [DOI: 10.1039/c5ra03979g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The interaction between the [(η6-p-cymene)Ru(benzaldehyde-N4-phenylthiosemicarbazone)Cl]Cl anticancer drug and ctDNA was systematically investigated by multispectroscopic and electrochemical studies.
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Affiliation(s)
- Shan Huang
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Fawei Zhu
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Qi Xiao
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Yu Liang
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Quan Zhou
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
| | - Wei Su
- College of Chemistry and Material Science
- Guangxi Teachers Education University
- Nanning 530001
- P. R. China
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28
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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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29
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Hu Q, Xu S. Sequence and Chiral Selectivity of Drug-DNA Interactions Revealed by Force Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Hu Q, Xu S. Sequence and Chiral Selectivity of Drug-DNA Interactions Revealed by Force Spectroscopy. Angew Chem Int Ed Engl 2014; 53:14135-8. [DOI: 10.1002/anie.201407093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Indexed: 01/25/2023]
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31
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Verebová V, Adamcik J, Danko P, Podhradský D, Miškovský P, Staničová J. Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA. Biochem Biophys Res Commun 2014; 444:50-5. [PMID: 24434150 DOI: 10.1016/j.bbrc.2014.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022]
Abstract
The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode.
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Affiliation(s)
- Valéria Verebová
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia
| | - Jozef Adamcik
- Food and Soft Materials Science, Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich, Switzerland
| | - Patrik Danko
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Dušan Podhradský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Pavol Miškovský
- Department of Biophysics, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Jana Staničová
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia.
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32
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Alonso-Sarduy L, Longo G, Dietler G, Kasas S. Time-lapse AFM imaging of DNA conformational changes induced by daunorubicin. NANO LETTERS 2013; 13:5679-5684. [PMID: 24125039 DOI: 10.1021/nl403361f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cancer is a major health issue that absorbs the attention of a large part of the biomedical research. Intercalating agents bind to DNA molecules and can inhibit their synthesis and transcription; thus, they are increasingly used as drugs to fight cancer. In this work, we show how atomic force microscopy in liquid can characterize, through time-lapse imaging, the dynamical influence of intercalating agents on the supercoiling of DNA, improving our understanding of the drug's effect.
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Affiliation(s)
- Livan Alonso-Sarduy
- Laboratoire de Physique de la Matière Vivante, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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33
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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
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34
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Dutta S, Snyder MJ, Rosile D, Binz KL, Roll EH, Suryadi J, Bierbach U, Guthold M. PT-ACRAMTU, a platinum-acridine anticancer agent, lengthens and aggregates, but does not stiffen or soften DNA. Cell Biochem Biophys 2013; 67:1103-13. [PMID: 23636685 PMCID: PMC3767762 DOI: 10.1007/s12013-013-9614-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We used atomic force microscopy (AFM) to study the dose-dependent change in conformational and mechanical properties of DNA treated with PT-ACRAMTU ([PtCl(en)(ACRAMTU-S)](NO3)2, (en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea. PT-ACRAMTU is the parent drug of a family of non-classical platinum-based agents that show potent activity in non-small cell lung cancer in vitro and in vivo. Its acridine moiety intercalates between DNA bases, while the platinum group forms mono-adducts with DNA bases. AFM images show that PT-ACRAMTU causes some DNA looping and aggregation at drug-to-base pair ratio (r b) of 0.1 and higher. Very significant lengthening of the DNA was observed with increasing doses of PT-ACRAMTU, and reached saturation at an r b of 0.15. At r b of 0.1, lengthening was 0.6 nm per drug molecule, which is more than one fully stretched base pair stack can accommodate, indicating that ACRAMTU also disturbs the stacking of neighboring base pair stacks. Analysis of the AFM images based on the worm-like chain (WLC) model showed that PT-ACRAMTU did not change the flexibility of (non-aggregated) DNA, despite the extreme lengthening. The persistence length of untreated DNA and DNA treated with PT-ACRAMTU was in the range of 49-65 nm. Potential consequences of the perturbations caused by this agent for the recognition and processing of the DNA adducts it forms are discussed.
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Affiliation(s)
- Samrat Dutta
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Matthew J. Snyder
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - David Rosile
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Kristen L. Binz
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Eric H. Roll
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Jimmy Suryadi
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109
| | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
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35
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Vanderlinden W, Blunt M, David CC, Moucheron C, Kirsch-De Mesmaeker A, De Feyter S. Mesoscale DNA Structural Changes on Binding and Photoreaction with Ru[(TAP)2PHEHAT]2+. J Am Chem Soc 2012; 134:10214-21. [DOI: 10.1021/ja303091q] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Willem Vanderlinden
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Matthew Blunt
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Charlotte C. David
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Cécile Moucheron
- Department of Chemistry, Laboratory
of Organic Chemistry and Photochemistry, Université Libre de Bruxelles, Avenue Franklin D. Roosevelt 50,
1050 Brussels, Belgium
| | - Andrée Kirsch-De Mesmaeker
- Department of Chemistry, Laboratory
of Organic Chemistry and Photochemistry, Université Libre de Bruxelles, Avenue Franklin D. Roosevelt 50,
1050 Brussels, Belgium
| | - Steven De Feyter
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
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36
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Banerjee T, Dubey P, Mukhopadhyay R. DNA compaction by mononuclear platinum cancer drug cisplatin and the trisplatinum anticancer agent BBR3464: Differences and similarities. Biochimie 2012; 94:494-502. [DOI: 10.1016/j.biochi.2011.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/24/2011] [Indexed: 10/17/2022]
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37
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Determining the binding mode and binding affinity constant of tyrosine kinase inhibitor PD153035 to DNA using optical tweezers. Biochem Biophys Res Commun 2010; 404:297-301. [PMID: 21130075 DOI: 10.1016/j.bbrc.2010.11.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 11/24/2010] [Indexed: 11/20/2022]
Abstract
Accurately predicting binding affinity constant (K(A)) is highly required to determine the binding energetics of the driving forces in drug-DNA interactions. Recently, PD153035, brominated anilinoquinazoline, has been reported to be not only a highly selective inhibitor of epidermal growth factor receptor but also a DNA intercalator. Here, we use a dual-trap optical tweezers to determining K(A) for PD153035, where K(A) is determined from the changes in B-form contour length (L) of PD153035-DNA complex. Here, L is fitted using a modified wormlike chain model. We found that a noticeable increment in L in 1 mM sodium cacodylate was exhibited. Furthermore, our results showed that K(A)=1.18(±0.09)×10(4) (1/M) at 23±0.5°C and the minimum distance between adjacent bound PD153035≈11 bp. We anticipate that by using this approach we can determine the complete thermodynamic profiles due to the presence of DNA intercalators.
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38
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Klajner M, Hebraud P, Sirlin C, Gaiddon C, Harlepp S. DNA Binding to an Anticancer Organo-Ruthenium Complex. J Phys Chem B 2010; 114:14041-7. [DOI: 10.1021/jp1044783] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcelina Klajner
- I.P.C.M.S., UMR7504, Université de Strasbourg, France, Wrocław University of Technology, Poland, Institut de Chimie, C.N.R.S., UMR7177, Université de Strasbourg, Synthèses Métallo-Induites, France, and INSERM U692-Université de Strasbourg, Signalisations Moléculaires et Neurodégénérescence, France
| | - Pascal Hebraud
- I.P.C.M.S., UMR7504, Université de Strasbourg, France, Wrocław University of Technology, Poland, Institut de Chimie, C.N.R.S., UMR7177, Université de Strasbourg, Synthèses Métallo-Induites, France, and INSERM U692-Université de Strasbourg, Signalisations Moléculaires et Neurodégénérescence, France
| | - Claude Sirlin
- I.P.C.M.S., UMR7504, Université de Strasbourg, France, Wrocław University of Technology, Poland, Institut de Chimie, C.N.R.S., UMR7177, Université de Strasbourg, Synthèses Métallo-Induites, France, and INSERM U692-Université de Strasbourg, Signalisations Moléculaires et Neurodégénérescence, France
| | - Christian Gaiddon
- I.P.C.M.S., UMR7504, Université de Strasbourg, France, Wrocław University of Technology, Poland, Institut de Chimie, C.N.R.S., UMR7177, Université de Strasbourg, Synthèses Métallo-Induites, France, and INSERM U692-Université de Strasbourg, Signalisations Moléculaires et Neurodégénérescence, France
| | - Sebastien Harlepp
- I.P.C.M.S., UMR7504, Université de Strasbourg, France, Wrocław University of Technology, Poland, Institut de Chimie, C.N.R.S., UMR7177, Université de Strasbourg, Synthèses Métallo-Induites, France, and INSERM U692-Université de Strasbourg, Signalisations Moléculaires et Neurodégénérescence, France
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39
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Atomic force microscopy study of DNA conformation in the presence of drugs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:59-68. [PMID: 20882274 DOI: 10.1007/s00249-010-0627-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 08/27/2010] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
Abstract
Binding of ligands to DNA gives rise to several relevant biological and biomedical effects. Here, through the use of atomic force microscopy (AFM), we studied the consequences of drug binding on the morphology of single DNA molecules. In particular, we quantitatively analyzed the effects of three different DNA-binding molecules (doxorubicin, ethidium bromide, and netropsin) that exert various pharmacologic and therapeutic effects. The results of this study show the consequences of intercalation and groove molecular binding on DNA conformation. These single-molecule measurements demonstrate morphological features that reflect the specific modes of drug-DNA interaction. This experimental approach may have implications in the design of therapeutically effective agents.
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40
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Lipfert J, Klijnhout S, Dekker NH. Torsional sensing of small-molecule binding using magnetic tweezers. Nucleic Acids Res 2010; 38:7122-32. [PMID: 20624816 PMCID: PMC2978369 DOI: 10.1093/nar/gkq598] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove binding anti-microbial drug; and topotecan, a clinically used anti-tumor drug. In the low-force limit in which biologically relevant torques can be accessed (<10 pN), we show that ethidium intercalation lengthens DNA ∼1.5-fold and decreases the persistence length, from which we extract binding constants. Using our control of supercoiling, we measure the decrease in DNA twist per intercalation to be 27.3 ± 1° and demonstrate that ethidium binding delays the accumulation of torsional stress in DNA, likely via direct reduction of the torsional modulus and torque-dependent binding. Furthermore, we observe that EtBr stabilizes the DNA duplex in regimes where bare DNA undergoes structural transitions. In contrast, minor groove binding by netropsin affects neither the contour nor persistence length significantly, yet increases the twist per base of DNA. Finally, we show that topotecan binding has consequences similar to those of EtBr, providing evidence for an intercalative binding mode. These insights into the torsional consequences of ligand binding can help elucidate the effects of small-molecule drugs in the cellular environment.
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Affiliation(s)
- Jan Lipfert
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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41
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Salerno D, Brogioli D, Cassina V, Turchi D, Beretta GL, Seruggia D, Ziano R, Zunino F, Mantegazza F. Magnetic tweezers measurements of the nanomechanical properties of DNA in the presence of drugs. Nucleic Acids Res 2010; 38:7089-99. [PMID: 20601682 PMCID: PMC2978368 DOI: 10.1093/nar/gkq597] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Herein, we study the nanomechanical characteristics of single DNA molecules in the presence of DNA binders, including intercalating agents (ethidium bromide and doxorubicin), a minor groove binder (netropsin) and a typical alkylating damaging agent (cisplatin). We have used magnetic tweezers manipulation techniques, which allow us to measure the contour and persistence lengths together with the bending and torsional properties of DNA. For each drug, the specific variations of the nanomechanical properties induced in the DNA have been compared. We observed that the presence of drugs causes a specific variation in the DNA extension, a shift in the natural twist and a modification of bending dependence on the imposed twist. By introducing a naive model, we have justified an anomalous correlation of torsion data observed in the presence of intercalators. Finally, a data analysis criterion for discriminating between different molecular interactions among DNA and drugs has been suggested.
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Affiliation(s)
- Domenico Salerno
- Dipartimento di Medicina Sperimentale, Universita' di Milano-Bicocca, via Cadore 48, Monza (MI) 20052, Italy.
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42
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Banerjee T, Dubey P, Mukhopadhyay R. Compacting effect of BBR3464, a new-generation trisplatinum anticancer agent, on DNA. Biochimie 2010; 92:846-51. [DOI: 10.1016/j.biochi.2010.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 01/18/2010] [Indexed: 11/26/2022]
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43
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Lubitz I, Zikich D, Kotlyar A. Specific high-affinity binding of thiazole orange to triplex and G-quadruplex DNA. Biochemistry 2010; 49:3567-74. [PMID: 20329708 DOI: 10.1021/bi1000849] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interaction of Thiazole Orange (TO) with double-, triple-, and quadruple-stranded forms of DNA was studied. We have demonstrated by UV-vis absorption, circular dichroism (CD), and fluorescence spectroscopy that TO binds with much higher affinity to triplex and G-quadruplex DNA structures compared to double-stranded (ds) DNA. Complexes of the dye with DNA triplexes and G-quadruplexes are very stable and do not dissociate during chromatography and gel electrophoresis. TO binding to either triple- or quadruple-stranded DNA structures results in a >1000-fold increase in dye fluorescence. The fluorescence titration data showed that TO to triad and tetrad ratios, in tight complexes with the triplex and the G-quadruplex, are equal to 0.5 and 1, respectively. Preferential binding of TO to triplexes and G-quadruplexes enables selective detection of only these DNA forms in gels in the absence of free TO in electrophoresis running buffer. We have also demonstrated that incubation of U2OS cells with submicromolar concentrations of TO results in preferential staining of certain areas in the nucleus in contrast to DAPI which binds to dsDNA and efficiently stains regions that are unstained with TO. We suggest that TO staining may be useful for the detection of noncanonical structural motifs in genomic DNA.
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Affiliation(s)
- Irit Lubitz
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
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44
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Yang TS, Cui Y, Wu CM, Lo JM, Chiang CS, Shu WY, Chung WJ, Yu CS, Chiang KN, Hsu IC. Determining the zero-force binding energetics of an intercalated DNA complex by a single-molecule approach. Chemphyschem 2010; 10:2791-4. [PMID: 19795434 DOI: 10.1002/cphc.200900435] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tzu-Sen Yang
- Institute of Biomedical Materials and Engineering, Taipei Medical University, Taipei 110, Taiwan
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45
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Abstract
The determination of the contour length of DNA imaged by either electron microscopy or atomic force microscopy is frequently required for investigating the physical properties of nucleic acids. Nevertheless, these measurements are often carried out with methods that are not optimized for the curvilinear shape of DNA or are too complex to be of practical use. The aim of this study is to provide a method for the contour length measurements of DNA that is accurate, practical, and computationally simple. Computer simulated DNA fragments were used as experimental benchmarks in order to compute the coefficients a and b of the (n(e), n(o))-characterization [L(n(e),n(o)) = an(e) + bn(o)] so as to minimize the error of the measurements. The data show that, at variance with straight lines, a DNA length estimator depends on both the DNA flexibility and the image resolution, but it is independent of the DNA contour length. A table with DNA estimators to be used for length measurements of digitized contours obtained under commonly used imaging conditions is provided. Although the method has been developed using DNA as a benchmark, its applicability can be extended to other polymers as well as to other imaging techniques.
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Affiliation(s)
- Claudio Rivetti
- Department of Biochemistry and Molecular Biology, University of Parma, Parma 43100, Italy.
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46
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47
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Arbuse A, Font M, Martínez MA, Fontrodona X, Prieto MJ, Moreno V, Sala X, Llobet A. DNA-Cleavage Induced by New Macrocyclic Schiff base Dinuclear Cu(I) Complexes Containing Pyridyl Pendant Arms. Inorg Chem 2009; 48:11098-107. [DOI: 10.1021/ic901488j] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Xavier Fontrodona
- Serveis Científico-Tècnics Universitat de Girona, Campus de Montilivi, E-17071 Girona, Spain
| | - Ma José Prieto
- Departament de Microbiologia Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain
| | | | - Xavier Sala
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, E-43007 Tarragona, Spain
| | - Antoni Llobet
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, E-43007 Tarragona, Spain
- Departament de Química, Universitat Autònoma de Barcelona, Ceranyola del Vallès, E-0194 Barcelona, Spain
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48
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Passeri R, Aloisi GG, Elisei F, Latterini L, Caronna T, Fontana F, Sora IN. Photophysical properties of N-alkylated azahelicene derivatives as DNA intercalators: counterion effects. Photochem Photobiol Sci 2009; 8:1574-82. [PMID: 19862416 DOI: 10.1039/b9pp00015a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, three compounds having the same organic moiety (N-methyl-5-azahelicenium salts) but different counterions (I-, NO3- and COOCF3-) have been investigated in buffered aqueous solutions and in the presence of DNA to give information on the counterion effects on the binding. In particular, the absorption spectra, fluorescence quantum yields and fluorescence lifetimes in aqueous solution for free organic molecules have been determined by steady-state and time-resolved spectrofluorimetric measurements. The obtained values are compared with those of the chromophores in the presence of increasing concentrations of DNA. The results allow determination of the association constants (K(a)) and the number of base couples per chromophore molecule (n) by means of the McGhee Von Hippel model. The binding parameters are strongly affected by the nature of counterions since the highest K(a) value was determined for the compound having COOCF3-; on the other hand the NO3- derivative is able to interact with the highest number of binding sites. The morphology and structural properties of the DNA-chromophore complexes were investigated by circular dichroism (CD) and atomic force microscopy (AFM). The data revealed that I- and COOCF3- derivatives preferentially form intercalation complexes, while the NO3- salt is able to form intercalation and grove binding complexes at the same time.
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Affiliation(s)
- Rosita Passeri
- Dipartimento di Chimica and Centro di Eccellenza Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto, 8, 06123, Perugia, Italy
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49
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Rocha MS. Modeling the entropic structural transition of DNA complexes formed with intercalating drugs. Phys Biol 2009; 6:036013. [DOI: 10.1088/1478-3975/6/3/036013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Adamcik J, Valle F, Witz G, Rechendorff K, Dietler G. The promotion of secondary structures in single-stranded DNA by drugs that bind to duplex DNA: an atomic force microscopy study. NANOTECHNOLOGY 2008; 19:384016. [PMID: 21832575 DOI: 10.1088/0957-4484/19/38/384016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We study the behavior of single-stranded DNA (ssDNA) in the presence of well-known drugs with either an intercalating binding mode, such as daunorubicin, actinomycin D, and chloroquine, or a minor groove binding mode, such as netropsin and berenil, by atomic force microscopy (AFM). At very low salt conditions, ssDNA molecules adopt an unstructured conformation without secondary structures. We observe that under these conditions additions of drugs that bind to double-stranded DNA (dsDNA) promote the formation of secondary structures in ssDNA. Furthermore, with an increase of concentration of the drugs, the extension as well as the thermal stabilization of these hairpins was observed.
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Affiliation(s)
- Jozef Adamcik
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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