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Pereira SAP, Romano-deGea J, Barbosa AI, Costa Lima SA, Dyson PJ, Saraiva MLMFS. Fine-tuning the cytotoxicity of ruthenium(II) arene compounds to enhance selectivity against breast cancers. Dalton Trans 2023; 52:11679-11690. [PMID: 37552495 PMCID: PMC10442743 DOI: 10.1039/d3dt02037a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023]
Abstract
Ruthenium-based complexes have been suggested as promising anticancer drugs exhibiting reduced general toxicity compared to platinum-based drugs. In particular, Ru(η6-arene)(PTA)Cl2 (PTA = 1,3,5-triaza-7-phosphaadamantane), or RAPTA, complexes have demonstrated efficacy against breast cancer by suppressing metastasis, tumorigenicity, and inhibiting the replication of the human tumor suppressor gene BRCA1. However, RAPTA compounds have limited cytotoxicity, and therefore comparatively high doses are required. This study explores the activity of a series of RAPTA-like ruthenium(II) arene compounds against MCF-7 and MDA-MB-231 breast cancer cell lines and [Ru(η6-toluene)(PPh3)2Cl]+ was identified as a promising candidate. Notably, [Ru(η6-toluene)(PPh3)2Cl]Cl was found to be remarkably stable and highly cytotoxic, and selective to breast cancer cells. The minor groove of DNA was identified as a relevant target.
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Affiliation(s)
- Sarah A P Pereira
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jan Romano-deGea
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Ana Isabel Barbosa
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
| | - Sofia A Costa Lima
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - M Lúcia M F S Saraiva
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
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2
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Cheng X, Huang J, Wang R, Xu Y, Wu N, Zhou J, Liu X, Wang H, Chen H. Inorganic-organic coprecipitation: spontaneous formation of enclosed and porous silica compartments with enriched biopolymers. NANOSCALE 2023; 15:2394-2401. [PMID: 36651126 DOI: 10.1039/d2nr05320a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We show that it is possible to spontaneously form all-enclosed compartments with microporous shells and enriched biopolymers via simple coprecipitation of silica and biopolymers. The reaction involves mild conditions and tolerates the random mixing of multiple reagents. Such a synthetic advance points to a new direction for resolving the chicken-egg dilemma of how the early life forms were hosted: without a physical barrier it would be difficult to maintain organized reactions, but without organized reactions, it would be difficult to create a cell membrane. In our synthesis, the divalent cation Ca2+ plays a critical role in the co-precipitation and in creating hollow compartments after simple dilution with water. The precursor of silica, poly(silicic acid), is a negatively charged, cross-linked polymer. It could be co-precipitated with negatively charged biopolymers such as DNA and proteins, whereas the remaining silica precursor forms a conformal and microporous shell on the surface of the initial precipitate. After etching, the biopolymers are retained inside the hollow compartments. The fact that multiple favorable conditions are easily brought together in enclosed compartments opens new possibilities in theorizing the host of early life forms.
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Affiliation(s)
- Xuejun Cheng
- Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Jie Huang
- Institute of Advanced Synthesis (IAS) and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
| | - Ruoxu Wang
- Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yue Xu
- Institute of Advanced Synthesis (IAS) and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
| | - Nan Wu
- State Key Laboratory of Materials Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Jie Zhou
- State Key Laboratory of Materials Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Xueyang Liu
- Institute of Advanced Synthesis (IAS) and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
| | - Hong Wang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Hongyu Chen
- Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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3
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Antonijevic M, Rochais C, Dallemagne P. C3-Symmetric Ligands in Drug Design: When the Target Controls the Aesthetics of the Drug. Molecules 2023; 28:molecules28020679. [PMID: 36677739 PMCID: PMC9862528 DOI: 10.3390/molecules28020679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
A number of proteins are able to adopt a homotrimeric spatial conformation. Among these structures, this feature appears as crucial for biologic targets, since it facilitates the design of C3-symmetric ligands that are especially suitable for displaying optimized ligand-target interactions and therapeutic benefits. Additionally, DNA as a therapeutic target, even if its conformation into a superhelix does not correspond to a C3-symmetry, can also take advantage of these C3-symmetric ligands for better interactions and therapeutic effects. For the moment, this opportunity appears to be under-exploited, but should become more frequent with the discovery of new homotrimeric targets such as the SARS-CoV2 spike protein. Besides their potential therapeutic interest, the synthetic access to these C3-symmetric ligands often leads to chemical challenges, although drug candidates with an aesthetic structure are generally obtained.
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4
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Tian Z, Ding T, Niu H, Mu Y, Xu N, Kong M, Zhang Y, Tian Z, Wu Y, Wang C. The substituent group effect: investigation of naphthalimide-spermidine conjugates binding to DNA by spectroscopy, molecular docking and dynamics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Sykes KS, White RJ. Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7322-7330. [PMID: 35639972 PMCID: PMC10150402 DOI: 10.1021/acs.langmuir.2c00840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The cation condensation-induced collapse of electrode-bound nucleic acids and the resulting change in the electrochemical signal is a useful tool to predict the structure and redox probe location of heterogeneous structures of surface-tethered DNA probes─a common architecture employed in the development of electrochemical sensors. In this paper, we measure the faradaic current of an appended redox molecule at the 3' position of the nucleic acid using cyclic voltammetry before and after nucleic acid collapse for various nucleic acid architectures and heterogeneous mixtures on the same electrode surface. The voltammetric peak current change with collapse correlates with the proximity of the redox molecules from the surface. For stem-loop probes, the terminal methylene blue is initially held closer to the surface, such that inducing collapse, by reducing the dielectric permittivity of the interrogation solution, results in a ∼30% increase in current. However, when incorporating pseudoknot probes that hold methylene blue further away from the electrode surface, the current change is much larger (∼120%), indicating a larger conformation change. Upon a 50:50 ratio of the two, we observe a change in current that relates to the ratiometric distribution of the probe used to make the surfaces. Additionally, using cyclic voltammetry, we find that the change between diffusion-limited and diffusion-independent peak currents is dependent upon the distinct structural characteristics of DNA probes on the surface (stem-loop or pseudoknot), as well as the ratios of different DNA probes on the surface. Thus, we demonstrate that the heterogeneous nature of DNA probes governs the corresponding electrochemical signals, which can lead to a better understanding on how to predict the structures of functional nucleic acids on electrode surfaces and how this affects surface-to-surface variability and electrochemical response.
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Affiliation(s)
- Kiana S. Sykes
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ryan J. White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Department of Electrical and Computer Engineering, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
- Corresponding Author:
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6
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Singh SB, Kumbhar AS, Walke G, Kulkarni PP. An insight into the morphology of DNA compaction induced by homobinuclear Ru(II) polypyridyl complexes. J Inorg Biochem 2022; 234:111870. [DOI: 10.1016/j.jinorgbio.2022.111870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
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7
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Paiva REF, Peterson EJ, Malina J, Zoepfl M, Hampton JD, Johnson WE, Graminha A, Ourahmane A, McVoy MA, Brabec V, Berners‐Price SJ, Farrell NP. On the Biology of Werner's Complex. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Raphael E. F. Paiva
- Institute for Glycomics Griffith University Gold Coast Campus Southport Qld. 4222 Australia
| | - Erica J. Peterson
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
- Massey Cancer Center Virginia Commonwealth University Richmond VA 23298-0037 USA
| | - Jaroslav Malina
- Institute of Biophysics Czech Academy of Sciences Kralovopolska 135 61265 Brno Czech Republic
| | - Mary Zoepfl
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - J. David Hampton
- Massey Cancer Center Virginia Commonwealth University Richmond VA 23298-0037 USA
- Department of Biochemistry and Molecular Biology Virginia Commonwealth University Richmond Virginia 23298-0033 USA
| | - Wyatt E. Johnson
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Angelica Graminha
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Amine Ourahmane
- Department of Pediatrics Virginia Commonwealth University Richmond VA 23298-0163 USA
| | - Michael A. McVoy
- Department of Pediatrics Virginia Commonwealth University Richmond VA 23298-0163 USA
| | - Viktor Brabec
- Institute of Biophysics Czech Academy of Sciences Kralovopolska 135 61265 Brno Czech Republic
| | - Susan J. Berners‐Price
- Institute for Glycomics Griffith University Gold Coast Campus Southport Qld. 4222 Australia
| | - Nicholas P. Farrell
- Institute for Glycomics Griffith University Gold Coast Campus Southport Qld. 4222 Australia
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
- Massey Cancer Center Virginia Commonwealth University Richmond VA 23298-0037 USA
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8
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de Paiva REF, Peterson EJ, Malina J, Zoepfl M, Hampton JD, Johnson WE, Graminha A, Ourahmane A, McVoy MA, Brabec V, Berners-Price SJ, Farrell NP. On the Biology of Werner's Complex. Angew Chem Int Ed Engl 2021; 60:17123-17130. [PMID: 34105220 PMCID: PMC8464317 DOI: 10.1002/anie.202105019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/30/2021] [Indexed: 11/05/2022]
Abstract
Werner's Complex, as a cationic coordination complex (CCC), has hitherto unappreciated biological properties derived from its binding affinity to highly anionic biomolecules such as glycosaminoglycans (GAGs) and nucleic acids. Competitive inhibitor and spectroscopic assays confirm the high affinity to GAGs heparin, heparan sulfate (HS), and its pentasaccharide mimetic Fondaparinux (FPX). Functional consequences of this affinity include inhibition of FPX cleavage by bacterial heparinase and mammalian heparanase enzymes with inhibition of cellular invasion and migration. Werner's Complex is a very efficient condensing agent for DNA and tRNA. In proof-of-principle for translational implications, it is demonstrated to display antiviral activity against human cytomegalovirus (HCMV) at micromolar concentrations with promising selectivity. Exploitation of non-covalent hydrogen-bonding and electrostatic interactions has motivated the unprecedented discovery of these properties, opening new avenues of research for this iconic compound.
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Affiliation(s)
- Raphael E F de Paiva
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Qld., 4222, Australia
| | - Erica J Peterson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, 23284-2006, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298-0037, USA
| | - Jaroslav Malina
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Mary Zoepfl
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, 23284-2006, USA
| | - J David Hampton
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298-0037, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, 23298-0033, USA
| | - Wyatt E Johnson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, 23284-2006, USA
| | - Angelica Graminha
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, 23284-2006, USA
| | - Amine Ourahmane
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, 23298-0163, USA
| | - Michael A McVoy
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, 23298-0163, USA
| | - Viktor Brabec
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Susan J Berners-Price
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Qld., 4222, Australia
| | - Nicholas P Farrell
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Qld., 4222, Australia
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, 23284-2006, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298-0037, USA
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9
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10
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Karami K, Ramezanpour A, Zakariazadeh M, Shahpiri A, Kharaziha M, Kazeminasab A. Luminescent Palladacycles Containing a Pyrene Chromophor; Synthesis, Biological and Computational Studies of the Interaction with DNA and BSA. ChemistrySelect 2019. [DOI: 10.1002/slct.201900707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Kazem Karami
- Department of ChemistryIsfahan University of Technology Isfahan 84156/83111 Iran
| | - Azar Ramezanpour
- Department of ChemistryIsfahan University of Technology Isfahan 84156/83111 Iran
| | - Mostafa Zakariazadeh
- Research Institute for Fundamental Sciences (RIFS) University of Tabriz Tabriz Iran
| | - Azar Shahpiri
- Department of BiotechnologyCollege of AgricultureIsfahan University of Technology Isfahan Iran
| | - Mahshid Kharaziha
- Department of Materials EngineeringIsfahan Univezrsity of Technology Isfahan Iran
| | - Akram Kazeminasab
- Department of BiotechnologyCollege of AgricultureIsfahan University of Technology Isfahan Iran
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11
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Sedighipoor M, Kianfar AH, Mohammadnezhad G, Görls H, Plass W, Momtazi-Borojeni AA, Abdollahi E. Synthesis, crystal structure of novel unsymmetrical heterocyclic Schiff base Ni(II)/V(IV) complexes: Investigation of DNA binding, protein binding and in vitro cytotoxic activity. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.12.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Zhang C, Zhang H, Han M, Yang X, Pei C, Xu Z, Du J, Li W, Chen S. DNA–affibody nanoparticle delivery system for cisplatin-based breast cancer chemotherapy. RSC Adv 2019; 9:1982-1989. [PMID: 35516156 PMCID: PMC9059769 DOI: 10.1039/c8ra08735k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/06/2019] [Indexed: 01/01/2023] Open
Abstract
Cisplatin is the most widely used anticancer drug, but its side effects limit the maximum systemic dose. To circumvent the side effects, a DNA tetrahedron–affibody nanoparticle was prepared by combination of a DNA chain with cisplatin via interstrand crosslinks or adducts. Each nanocarrier can bind ∼68 molecules of cisplatin. This cisplatin nanoparticle exhibited high selectivity and inhibition for breast cancer HER2 overexpressing cells BT474 and lower toxicity in MCF-7 cells with low HER2 expression. The nano-drug inhibited the growth of BT474 cells by 94.57% at 512 nM (containing 33.3 μM cisplatin), which was higher than that of cisplatin (82.9%, 33.3 μM). The novel nano-drug cisplatin-DNA tetrahedron-affibody has high specificity, high efficacy, and low toxicity for the treatment of HER2-overexpressing breast cancers.![]()
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Affiliation(s)
- Chao Zhang
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - HongLei Zhang
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - MengNan Han
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - XueLi Yang
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - ChaoHong Pei
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - ZhiDong Xu
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - Jie Du
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - Wei Li
- Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education
- College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- China
| | - Shengxi Chen
- Center for BioEnergetics
- Biodesign Institute
- Arizona State University
- Tempe 85287
- USA
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13
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Ethanol effect on gold nanoparticle aggregation state and its implication in the interaction mechanism with DNA. J Colloid Interface Sci 2018; 529:65-76. [DOI: 10.1016/j.jcis.2018.05.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 01/08/2023]
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14
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Modulation of probe-genomic DNA interaction within the confined interior of a reverse micelle: Is the bulk-like properties of water truly achieved in large reverse micelles? Int J Biol Macromol 2018; 118:1203-1210. [PMID: 29969635 DOI: 10.1016/j.ijbiomac.2018.06.180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/29/2018] [Accepted: 06/28/2018] [Indexed: 11/20/2022]
Abstract
The prime motivation of the present study is to explore the effect of reverse micellar confinement on the binding interaction of an anthracene-based probe 9-methyl anthroate with herring-sperm DNA. The structural modification of the genomic DNA from its native B-form to the non-native C-form and subsequently to the condensed Ψ-form as a function of the level of hydration (W0, defined as [water] / [surfactant]) of the reverse micellar core is found to reveal a remarkable regulatory role on the stability of the stacking interaction (intercalation) of the probe within the DNA helix; the interaction being progressively stabilized at higher W0. Particularly, a close perusal of the dynamical aspects of the interaction is found to be counter-intuitive to the popular notion of the properties of the confined water within the reverse micelles typically approaching bulk-like properties at sufficiently high hydration levels (W0 > 10).
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15
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Nishio T, Yoshikawa Y, Fukuda W, Umezawa N, Higuchi T, Fujiwara S, Imanaka T, Yoshikawa K. Branched-Chain Polyamine Found in Hyperthermophiles Induces Unique Temperature-Dependent Structural Changes in Genome-Size DNA. Chemphyschem 2018; 19:2299-2304. [PMID: 29931720 PMCID: PMC6175440 DOI: 10.1002/cphc.201800396] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/31/2022]
Abstract
A pentavalent branched‐chain polyamine, N4‐bis(aminopropyl)spermidine 3(3)(3)4, is a unique polycation found in the hyperthermophilic archaeon Thermococcus kodakarensis, which grows at temperatures between 60 and 100 °C. We studied the effects of this branched‐chain polyamine on DNA structure at different temperatures up to 80 °C. Atomic force microscopic observation revealed that 3(3)(3)4 induces a mesh‐like structure on a large DNA (166 kbp) at 24 °C. With an increase in temperature, DNA molecules tend to unwind, and multiple nano‐loops with a diameter of 10–50 nm are generated along the DNA strand at 80 °C. These results were compared to those obtained with linear‐chain polyamines, homocaldopentamine 3334 and spermidine, the former of which is a structural isomer of 3(3)(3)4. These specific effects are expected to neatly concern with its role on high‐temperature preference in hyperthermophiles.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Wakao Fukuda
- School of Science and Technology, Kwansei-gakuin University, Sanda, 669-1337, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shinsuke Fujiwara
- School of Science and Technology, Kwansei-gakuin University, Sanda, 669-1337, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
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16
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Kankia B. Monomolecular tetrahelix of polyguanine with a strictly defined folding pattern. Sci Rep 2018; 8:10115. [PMID: 29973629 PMCID: PMC6031693 DOI: 10.1038/s41598-018-28572-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/25/2018] [Indexed: 11/10/2022] Open
Abstract
The G3TG3TG3TG3 (G3T) sequence folds into a monomolecular quadruplex with all-parallel G3 segments connected to each other by chain-reversal loops. The homopolymer consisting of n number of G3T domains directly conjugated to each other folds into an uninterrupted and unusually stable polymer, tetrahelical monomolecular DNA (tmDNA). It was demonstrated that the tmDNA architecture has strong potential in nanotechnologies as highly programmable building material, high affinity coupler and the driving force for endergonic reactions. Here, we explore capability of analogous DNA sequences (i.e., monomolecular quadruplexes with G2 or G4 segments) to construct tmDNA architecture. The study demonstrates that tmDNA can have only one building pattern based on a quadruplex domain with three G-tetrads and single-nucleotide loops, G3N (N = G, A, C and T); all other domains demonstrate antiparallel topologies unsuitable for tmDNA. The present study also suggests that polyguanine is capable of tmDNA formation with strictly defined building pattern; G3 segments connected to each other by chain-reversal G-loops. These findings can have significant impact on (i) DNA nanotechnologies; (ii) structure prediction of G-rich sequences of genome; and (iii) modeling of abiogenesis.
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Affiliation(s)
- Besik Kankia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
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17
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Marazzi M, Gattuso H, Monari A, Assfeld X. Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules. Front Chem 2018; 6:86. [PMID: 29666792 PMCID: PMC5891624 DOI: 10.3389/fchem.2018.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/12/2018] [Indexed: 01/05/2023] Open
Abstract
Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.
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Affiliation(s)
- Marco Marazzi
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Logroño, Spain
| | - Hugo Gattuso
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
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18
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Sett R, Sen S, Paul BK, Guchhait N. How Does Nanoconfinement within a Reverse Micelle Influence the Interaction of Phenazinium-Based Photosensitizers with DNA? ACS OMEGA 2018; 3:1374-1385. [PMID: 31458466 PMCID: PMC6641382 DOI: 10.1021/acsomega.7b01820] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/17/2018] [Indexed: 06/10/2023]
Abstract
The major focus of the present work lies in exploring the influence of nanoconfinement within aerosol-OT (AOT) reverse micelles on the binding interaction of two phenazinium-based photosensitizers, namely, phenosafranin (PSF) and safranin-O (SO), with the DNA duplex. Circular dichroism and dynamic light-scattering studies reveal the condensation of DNA within the reverse micellar interior (transformation of the B-form of native DNA to ψ-form). Our results unveil a remarkable effect of the degree of hydration of the reverse micellar core on the stability of the stacking interaction (intercalation) of the drugs (PSF and SO) into DNA; increasing size of the water nanopool (that is, w 0) accompanies decreasing curvature of the DNA duplex structure with the consequent effect of increasing stabilization of the drug:DNA intercalation. The marked differences in the dynamical aspects of the interaction scenario following encapsulation within the reverse micellar core and the subsequent dependence on the size of the water nanopool are also meticulously explored. The differential degrees of steric interactions offered by the drug molecules (presence of methyl substitutions on the planar phenazinium ring in SO) are also found to affect the extent of intercalation of the drugs to DNA. In this context, it is imperative to state that the water pool of the reverse micellar core is often argued to approach bulk-like properties of water with increasing micellar size (typically w 0 ≥ 10), so that deviation from the bulk water properties is likely to be minimized in large reverse micelles (w 0 ≥ 10). On the contrary, our results (particularly quantitative elucidation of micropolarity and dynamical aspects of the interaction) explicitly demonstrate that the bulk-like behavior of the nanoconfined water is not truly achieved even in large reverse micelles.
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Affiliation(s)
- Riya Sett
- Department
of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
| | - Swagata Sen
- Department
of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
| | - Bijan K. Paul
- Department
of Chemistry, Mahadevananda Mahavidyalaya, Barrackpore, Kolkata 700120, India
| | - Nikhil Guchhait
- Department
of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, India
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19
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Katner SJ, Johnson WE, Peterson EJ, Page P, Farrell NP. Comparison of Metal-Ammine Compounds Binding to DNA and Heparin. Glycans as Ligands in Bioinorganic Chemistry. Inorg Chem 2018; 57:3116-3125. [PMID: 29473748 DOI: 10.1021/acs.inorgchem.7b03043] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present spectroscopic and biophysical approaches to examine the affinity of metal-ammine coordination complexes for heparin as a model for heparan sulfate (HS). Similar to nucleic acids, the highly anionic nature of heparin means it is associated in vivo with physiologically relevant cations, and this work extends their bioinorganic chemistry to substitution-inert metal-ammine compounds (M). Both indirect and direct assays were developed. M compounds are competitive inhibitors of methylene blue (MB)-heparin binding, and the change in the absorbance of the dye in the presence or absence of heparin can be used as an indirect reporter of M-heparin affinity. A second indirect assay uses the change in fluorescence of TAMRA-R9, a nonaarginine linked to a fluorescent TAMRA moiety, as a reporter for M-heparin binding. Direct assays are surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). The Kd values for TriplatinNC-heparin varied to some extent depending on the technique from 33.1 ± 2 nM (ITC) to 66.4 ± 1.3 nM (MB absorbance assay) and 340 ± 30 nM (SPR). The differences are explained by the nature of the technique and the use of heparin of differing molecular weight. Indirect probes using the displacement of ethidium bromide from DNA or, separately, fluorescently labeled oligonucleotide (DNA-Fl) can measure the relative affinities of heparin and DNA for M compounds. These assays showed essentially equivalent affinity of TriplatinNC for heparin and DNA. The generality of these methods was confirmed with a series of mononuclear cobalt, ruthenium, and platinum compounds with significantly lower affinity because of their smaller overall positive charge but in the order [Co(NH3)6]3+ > [Ru(NH3)6]3+ > [Pt(NH3)4]2+. The results on heparin can be extrapolated to glycosoaminoglycans such as HS, emphasizing the relevance of glycan interactions in understanding the biological properties of coordination compounds and the utility of the metalloglycomics concept for extending bioinorganic chemistry to this class of important biomolecules.
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Affiliation(s)
- Samantha J Katner
- Department of Chemistry and Massey Cancer Center , Virginia Commonwealth University (VCU) , Richmond , Virginia 23284 , United States
| | - Wyatt E Johnson
- Department of Chemistry and Massey Cancer Center , Virginia Commonwealth University (VCU) , Richmond , Virginia 23284 , United States
| | - Erica J Peterson
- Department of Chemistry and Massey Cancer Center , Virginia Commonwealth University (VCU) , Richmond , Virginia 23284 , United States
| | - Phillip Page
- Reichert Technologies , Depew , New York 14043 , United States
| | - Nicholas P Farrell
- Department of Chemistry and Massey Cancer Center , Virginia Commonwealth University (VCU) , Richmond , Virginia 23284 , United States
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20
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Karami K, Rafiee M, Lighvan ZM, Zakariazadeh M, Faal AY, Esmaeili SA, Momtazi-Borojeni AA. Synthesis, spectroscopic characterization and in vitro cytotoxicities of new organometallic palladium complexes with biologically active β-diketones; Biological evaluation probing of the interaction mechanism with DNA/Protein and molecular docking. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Lozano HJ, Busto N, Lari M, Leal JM, García B. Binding of aluminium/cacodylate complexes with DNA and RNA. Experimental and “in silico”study. NEW J CHEM 2018. [DOI: 10.1039/c8nj01779d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mechanism of the interaction of a dinuclear aluminium/cacodylate complex with nucleic acids.
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Affiliation(s)
- H. J. Lozano
- Chemistry Department
- University of Burgos
- Burgos
- Spain
| | - N. Busto
- Chemistry Department
- University of Burgos
- Burgos
- Spain
| | - M. Lari
- Chemistry Department
- University of Burgos
- Burgos
- Spain
| | - J. M. Leal
- Chemistry Department
- University of Burgos
- Burgos
- Spain
| | - B. García
- Chemistry Department
- University of Burgos
- Burgos
- Spain
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22
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Li X, Sun D, Chen Y, Wang K, He Q, Wang G. Studying compaction-decompaction of DNA molecules induced by surfactants. Biochem Biophys Res Commun 2017; 495:2559-2565. [PMID: 29288663 DOI: 10.1016/j.bbrc.2017.12.151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 11/30/2022]
Abstract
The mechanism and detailed processes of DNA compaction and decompaction are essential for the life activities, as well as for the researches in the molecular biology, genetics and biomedicine. The compaction of two kinds of DNA molecules caused by Cetyltrimethyl Ammonium Bromide (CTAB) and their decompaction induced with sodium dodecyl sulfate (SDS) or excessive amount of CTAB have been investigated with multiple perspectives such as the UV-VIS spectrophotometry, dynamic light scattering, and zeta potential. The compaction phenomenon of DNA can easily be observed when the CTAB combines with the DNA, not just when the molar ratio QCTAB/QDNA is approximately equal to 1 as the conventional recognition, but also when QCTAB/QDNA <1,DNA can be compacted; Molecular state of DNA is only changed in the conformational structure, but not in the chemical structure. Finally, a model is suggested to help catch on the biophysical mechanism of DNA chain conformational change.
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Affiliation(s)
- Xiaoyan Li
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China; Physics Department, Northwest University, Xi'an 710069, China
| | - Dan Sun
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China
| | - Yanyan Chen
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China
| | - Kaige Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China.
| | - Qingli He
- Physics Department, Northwest University, Xi'an 710069, China
| | - Guiren Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China; Mechanical Engineering Department & Biomedical Engineering Program, University of South Carolina, Columbia SC 29208, USA
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23
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Zou S, Li G, Rees TW, Jin C, Huang J, Chen Y, Ji L, Chao H. Interfering with DNA High-Order Structures using Chiral Ruthenium(II) Complexes. Chemistry 2017; 24:690-698. [PMID: 29112314 DOI: 10.1002/chem.201704403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Indexed: 12/31/2022]
Abstract
In this work, it was found that DNA can undergo B-Z transformational changes and compaction in the presence of DNA intercalators such as ruthenium(II) polypyridyl complexes. The link between B-Z transition and condensation is weak but can be strengthened under certain circumstances with slight alterations to the structures of the ruthenium(II) complexes. Here, following on from previous research, this work reports a series of ruthenium(II) complexes with imidazophenanthroline ligands, which vary in size and planarity. The complexes exhibit distinct effects on DNA structures, ranging from little impact to the transformation of DNA secondary structures to the formation of higher-order DNA structures. Further studies on DNA morphological changes induced by chiral ruthenium(II) complexes are observed by atomic force microscopy and transmission electron microscopy.
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Affiliation(s)
- Shanshan Zou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Guanying Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Thomas W Rees
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Chengzhi Jin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Juanjuan Huang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Yu Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
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24
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Tian Z, Cui H, Liu H, Dong J, Dong H, Zhao L, Li X, Zhang Y, Huang Y, Song L, Bian L, Wang Y, Xu X, Wang C. Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking. MEDCHEMCOMM 2017; 8:2079-2092. [PMID: 30108725 PMCID: PMC6072523 DOI: 10.1039/c7md00389g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/26/2017] [Indexed: 01/23/2023]
Abstract
The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Hailong Cui
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - He Liu
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Jun Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Huanyang Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Luyao Zhao
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xueting Li
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yan Zhang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yingying Huang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Lina Song
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Longxiang Bian
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Yuxia Wang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xuejun Xu
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
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25
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Vittala SK, Saraswathi SK, Joseph J. Fullerene Cluster Assisted Self-Assembly of Short DNA Strands into Semiconducting Nanowires. Chemistry 2017; 23:15759-15765. [PMID: 28858402 DOI: 10.1002/chem.201703333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 01/02/2023]
Abstract
Programmable, hierarchical assembly of DNA nanostructures with precise organisation of functional components have been demonstrated previously with tiled assembly and DNA origami. However, building organised nanostructures with random oligonucleotide strands remains as an elusive problem. Herein, a simple and general strategy, in which nanoclusters of a fullerene derivative act as stapler motifs in bringing ordered nanoscale assembly of short oligonucleotide duplexes into micrometre-sized nanowires, is described. In this approach, the fullerene derivative, by virtue of its amphiphilic structure and unique hydrophobic-hydrophilic balance, pre-assembles to form 3-5 nm sized clusters in a mixture of DMSO-phosphate buffer, which further assists the assembly of DNA strands. The optimum cluster size, availability of DNA anchoring motifs and the nature of the DNA strands controls the structure of these nanomaterials. Furthermore, horizontal conductivity measurements through conductive AFM confirmed the charge transport properties of these nanowires. The current strategy could be employed to organise random DNA duplexes and tiles into functional nanostructures, and hence, open up new avenues in DNA nanotechnology.
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Affiliation(s)
- Sandeepa Kulala Vittala
- Photosciences and Photonics Section, CSIR, National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST Campus, Thiruvananthapuram, Kerala, 695019, India
| | - Sajena Kanangat Saraswathi
- Photosciences and Photonics Section, CSIR, National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST Campus, Thiruvananthapuram, Kerala, 695019, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR, National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NIIST Campus, Thiruvananthapuram, Kerala, 695019, India
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26
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Sun T, Mirzoev A, Korolev N, Lyubartsev AP, Nordenskiöld L. All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine. J Phys Chem B 2017; 121:7761-7770. [DOI: 10.1021/acs.jpcb.7b03793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Tiedong Sun
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander Mirzoev
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Nikolay Korolev
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander P. Lyubartsev
- Department
of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Nordenskiöld
- School
of Biological Sciences, Nanyang Technological University, Singapore 637551
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27
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Selective colorimetric analysis of spermine based on the cross-linking aggregation of gold nanoparticles chain assembly. Talanta 2017; 167:193-200. [DOI: 10.1016/j.talanta.2017.01.085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 11/21/2022]
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28
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Upadhyay SK. Binding and thermodynamics of REV peptide-ctDNA interaction. Biopolymers 2017; 108. [PMID: 27353011 DOI: 10.1002/bip.22902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/13/2016] [Accepted: 06/25/2016] [Indexed: 02/04/2023]
Abstract
The thermodynamics of DNA-ligand binding is important as it provides useful information to understand the details of binding processes. HIV-1 REV response element (RRE) located in the env coding region of the viral genome is reported to be well conserved across different HIV-1 isolates. In this study, the binding characteristics of Calf thymus DNA (ctDNA) and REV peptide from HIV-1 were investigated using spectroscopic (UV-visible, fluorescence, and circular dichroism (CD)) and isothermal titration calorimetric (ITC) techniques. Thermal stability and ligand binding properties of the ctDNA revealed that native ctDNA had a Tm of 75.5 °C, whereas the ctDNA-REV peptide complex exhibited an incremental shift in the Tm by 8 °C, indicating thermal stability of the complex. CD data indicated increased ellipticity due to large conformational changes in ctDNA molecule upon binding with REV peptide and two binding stoichiometric modes are apparent. The ctDNA experienced condensation due to large conformational changes in the presence of REV peptide and positive B→Ψ transition was observed at higher molar charge ratios. Fluorescence studies performed at several ligand concentrations revealed a gradual decrease in the fluorescence intensity of EtBr-bound ctDNA in response to increasing ligand concentrations. The fluorescence data further confirmed two stoichiometric modes of binding for ctDNA-REV peptide complex as previously observed with CD studies. The binding enthalpies were determined using ITC in the temperature range of 293 K-308 K. The ITC binding isotherm was exothermic at all temperatures examined, with low ΔH values indicating that the ctDNA-REV peptide interaction is driven largely by entropy. The heat capacity change (ΔCp ) was insignificant, an unusual finding in the area of DNA-peptide interaction studies. The variation in the values obtained for ΔH, ΔS, and ΔG with temperature further suggests that ctDNA-REV peptide interaction is entropically driven. ITC based analysis of salt dependence of binding constant gave a charge value (Z) = +4.01, as determined for the δlnK/δln[Na+ ] parameter, suggesting the participation of only 3-4 Arg out of 11 Arg charge from REV peptide. The stoichiometry observed for the complex was three molar charge of REV peptide binding per molar charge of ctDNA. ITC based analysis further confirmed that the binding between ctDNA and REV peptide is governed by electrostatic interaction. Molecular interactions including H-bonding, van der Waals forces, and solvent molecules rearrangement, underlie the binding of REV peptide to ctDNA.
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29
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Tian Z, Zhao L, Dong H, Zhang Y, Zhang Y, Ren Q, Shao S, Huang Y, Song L, Guo T, Xu X, Wang C. Study on the interaction of anthracenyl-methyl homospermidine conjugate (ANTMHspd) with DNA by spectroscopic methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 169:27-34. [DOI: 10.1016/j.jphotobiol.2017.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/21/2017] [Indexed: 11/16/2022]
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30
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Goodman AM, Hogan NJ, Gottheim S, Li C, Clare SE, Halas NJ. Understanding Resonant Light-Triggered DNA Release from Plasmonic Nanoparticles. ACS NANO 2017; 11:171-179. [PMID: 28114757 DOI: 10.1021/acsnano.6b06510] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nanoparticle-based platforms for gene therapy and drug delivery are gaining popularity for cancer treatment. To improve therapeutic selectivity, one important strategy is to remotely trigger the release of a therapeutic cargo from a specially designed gene- or drug-laden near-infrared (NIR) absorbing gold nanoparticle complex with NIR light. While there have been multiple demonstrations of NIR nanoparticle-based release platforms, our understanding of how light-triggered release works in such complexes is still limited. Here, we investigate the specific mechanisms of DNA release from plasmonic nanoparticle complexes using continuous wave (CW) and femtosecond pulsed lasers. We find that the characteristics of nanoparticle-based DNA release vary profoundly from the same nanoparticle complex, depending on the type of laser excitation. CW laser illumination drives the photothermal release of dehybridized single-stranded DNA, while pulsed-laser excitation results in double-stranded DNA release by cleavage of the Au-S bond, with negligible local heating. This dramatic difference in DNA release from the same DNA-nanoparticle complex has very important implications in the development of NIR-triggered gene or drug delivery nanocomplexes.
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Affiliation(s)
| | | | | | | | - Susan E Clare
- Department of Surgery, Feinberg School of Medicine, Northwestern University , Chicago, Illinois 60611, United States
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31
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McStay N, Molphy Z, Coughlan A, Cafolla A, McKee V, Gathergood N, Kellett A. C 3-symmetric opioid scaffolds are pH-responsive DNA condensation agents. Nucleic Acids Res 2016; 45:527-540. [PMID: 27899572 PMCID: PMC5314759 DOI: 10.1093/nar/gkw1097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/11/2016] [Accepted: 10/27/2016] [Indexed: 01/28/2023] Open
Abstract
Herein we report the synthesis of tripodal C3-symmetric opioid scaffolds as high-affinity condensation agents of duplex DNA. Condensation was achieved on both supercoiled and canonical B-DNA structures and identified by agarose electrophoresis, viscosity, turbidity and atomic force microscopy (AFM) measurements. Structurally, the requirement of a tris-opioid scaffold for condensation is demonstrated as both di- (C2-symmetric) and mono-substituted (C1-symmetric) mesitylene-linked opioid derivatives poorly coordinate dsDNA. Condensation, observed by toroidal and globule AFM aggregation, arises from surface-binding ionic interactions between protonated, cationic, tertiary amine groups on the opioid skeleton and the phosphate nucleic acid backbone. Indeed, by converting the 6-hydroxyl group of C3-morphine (MC3) to methoxy substituents in C3-heterocodeine (HC3) and C3-oripavine (OC3) molecules, dsDNA compaction is retained thus negating the possibility of phosphate—hydroxyl surface-binding. Tripodal opioid condensation was identified as pH dependent and strongly influenced by ionic strength with further evidence of cationic amine-phosphate backbone coordination arising from thermal melting analysis and circular dichroism spectroscopy, with compaction also witnessed on synthetic dsDNA co-polymers poly[d(A-T)2] and poly[d(G-C)2]. On-chip microfluidic analysis of DNA condensed by C3-agents provided concentration-dependent protection (inhibition) to site-selective excision by type II restriction enzymes: BamHI, HindIII, SalI and EcoRI, but not to the endonuclease DNase I.
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Affiliation(s)
- Natasha McStay
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Alan Coughlan
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Attilio Cafolla
- School of Physical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nicholas Gathergood
- Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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32
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Singh SB, Kumbhar AS, Khan A. Honeycomb-like Ordered Assembly of DNA Induced by Flexible Binuclear Ruthenium(II)-Polypyridyl Complexes. Chemistry 2016; 22:15760-15771. [DOI: 10.1002/chem.201602488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/10/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Sushma B. Singh
- Department of Chemistry; Savitribai Phule Pune University; Pune- 411007 India
| | - Avinash S. Kumbhar
- Department of Chemistry; Savitribai Phule Pune University; Pune- 411007 India
| | - Ayesha Khan
- Department of Chemistry; Savitribai Phule Pune University; Pune- 411007 India
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Biomolecular interaction, catecholase like activity and alkane oxidation in ionic liquids of a phenylcarbohydrazone-based monocopper(II) complex. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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Zhang Z, Zhao Y, Meng X, Zhao D, Zhang D, Wang L, Liu C. A Simple Zn2+ Complex-Based Composite System for Efficient Gene Delivery. PLoS One 2016; 11:e0158766. [PMID: 27433798 PMCID: PMC4951035 DOI: 10.1371/journal.pone.0158766] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/21/2016] [Indexed: 11/19/2022] Open
Abstract
Metal complexes might become a new type of promising gene delivery systems because of their low cytotoxicity, structural diversity, controllable aqua- and lipo-solubility, and appropriate density and distribution of positive charges. In this study, Zn2+ complexes (1-10) formed with a series of ligands contained benzimidazole(bzim)were prepared and characterized. They were observed to have different affinities for DNA, dependent on their numbers of positive charges, bzim groups, and coordination structures around Zn2+. The binding induced DNA to condensate into spherical nanoparticles with ~ 50 nm in diameter. The cell transfection efficiency of the DNA nanoparticles was poor, although they were low toxic. The sequential addition of the cell-penetrating peptide (CPP) TAT(48-60) and polyethylene glycol (PEG) resulted in the large DNA condensates (~ 100 nm in diameter) and the increased cellular uptake. The clathrin-mediated endocytosis was found to be a key cellular uptake pathway of the nanoparticles formed with or without TAT(48-60) or/and PEG. The DNA nanoparticles with TAT(48-60) and PEG was found to have the cell transfection efficiency up to 20% of the commercial carrier Lipofect. These results indicated that a simple Zn2+-bzim complex-based composite system can be developed for efficient and low toxic gene delivery through the combination with PEG and CPPs such as TAT.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Yanjie Zhao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Xianggao Meng
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Dan Zhao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Dan Zhang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Li Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
- * E-mail: (CL); (LW)
| | - Changlin Liu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education and School of Chemistry, Central China Normal University, Wuhan, 430079, China
- * E-mail: (CL); (LW)
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35
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Frutos MD, Leforestier A, Degrouard J, Zambrano N, Wien F, Boulanger P, Brasilès S, Renouard M, Durand D, Livolant F. Can Changes in Temperature or Ionic Conditions Modify the DNA Organization in the Full Bacteriophage Capsid? J Phys Chem B 2016; 120:5975-86. [PMID: 27152667 DOI: 10.1021/acs.jpcb.6b01783] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We compared four bacteriophage species, T5, λ, T7, and Φ29, to explore the possibilities of DNA reorganization in the capsid where the chain is highly concentrated and confined. First, we did not detect any change in DNA organization as a function of temperature between 20 to 40 °C. Second, the presence of spermine (4+) induces a significant enlargement of the typical size of the hexagonal domains in all phages. We interpret these changes as a reorganization of DNA by slight movements of defects in the structure, triggered by a partial screening of repulsive interactions. We did not detect any signal characteristic of a long-range chiral organization of the encapsidated DNA in the presence and in the absence of spermine.
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Affiliation(s)
- Marta de Frutos
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Amélie Leforestier
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Jéril Degrouard
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Nebraska Zambrano
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Frank Wien
- Synchrotron SOLEIL, DISCO, L'Orme des Merisiers , 91190 St Aubin, France
| | - Pascale Boulanger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Sandrine Brasilès
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Madalena Renouard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Françoise Livolant
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
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36
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Singh AK, Saxena G, Dixit S, Hamidullah, Singh SK, Singh SK, Arshad M, Konwar R. Synthesis, characterization and biological activities of some Ru(II) complexes with substituted chalcones and their applications as chemotherapeutics against breast cancer. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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37
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Tian Z, Huang Y, Zhang Y, Song L, Qiao Y, Xu X, Wang C. Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:1-15. [PMID: 26926663 DOI: 10.1016/j.jphotobiol.2016.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
Abstract
The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yingying Huang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Zhang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Lina Song
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Qiao
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; State Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuejun Xu
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
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38
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Biswas N, Chakraborty S, Datta A, Sarkar M, Mukhopadhyay MK, Bera MK, Seto H. Counterion effects on nano-confined metal-drug-DNA complexes. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:62-7. [PMID: 26925353 PMCID: PMC4734432 DOI: 10.3762/bjnano.7.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
We have explored morphology of DNA molecules bound with Cu complexes of piroxicam (a non-steroidal anti-inflammatory drug) molecules under one-dimensional confinement of thin films and have studied the effect of counterions present in a buffer. X-ray reflectivity at and away from the Cu K absorption edge and atomic force microscopy studies reveal that confinement segregates the drug molecules preferentially in a top layer of the DNA film, and counterions enhance this segregation.
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Affiliation(s)
- Nupur Biswas
- Surface Physics and Material Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- present affiliation: Soft Condensed Matter Department, Raman Research Institute, Bangalore 560080, India
| | - Sreeja Chakraborty
- Chemical Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Alokmay Datta
- Surface Physics and Material Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Munna Sarkar
- Chemical Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Mrinmay K Mukhopadhyay
- Surface Physics and Material Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Mrinal K Bera
- Center for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637, USA
| | - Hideki Seto
- KENS & CMRC, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
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39
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Agudelo D, Kreplak L, Tajmir-Riahi HA. tRNA conjugation with chitosan nanoparticles: An AFM imaging study. Int J Biol Macromol 2015; 85:150-6. [PMID: 26723249 DOI: 10.1016/j.ijbiomac.2015.12.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 02/06/2023]
Abstract
The conjugation of tRNA with chitosan nanoparticles of different sizes 15,100 and 200 kDa was investigated in aqueous solution using multiple spectroscopic methods and atomic force microscopy (AFM). Structural analysis showed that chitosan binds tRNA via G-C and A-U base pairs as well as backbone PO2 group, through electrostatic, hydrophilic and H-bonding contacts with overall binding constants of KCh-15-tRNA=4.1 (±0.60)×10(3)M(-1), KCh-100-tRNA=5.7 (±0.8)×10(3)M(-1) and KCh-200-tRNA=1.2 (±0.3)×10(4)M(-1). As chitosan size increases more stable polymer-tRNA conjugate is formed. AFM images showed major tRNA aggregation and particle formation occurred as chitosan concentration increased. Even though chitosan induced major biopolymer structural changes, tRNA remains in A-family structure.
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Affiliation(s)
- D Agudelo
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada
| | - L Kreplak
- Department of Physics and Atmospheric Science, Sir James Dunn Building Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H4R2, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada.
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40
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Agudelo D, Kreplak L, Tajmir-Riahi HA. Microscopic and spectroscopic analysis of chitosan-DNA conjugates. Carbohydr Polym 2015; 137:207-213. [PMID: 26686122 DOI: 10.1016/j.carbpol.2015.09.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 08/31/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022]
Abstract
Conjugations of DNA with chitosans 15 kD (ch-15), 100 kD (ch-100) and 200 kD (ch-200) were investigated in aqueous solution at pH 5.5-6.5. Multiple spectroscopic methods and atomic force microscopy (AFM) were used to locate the chitosan binding sites and the effect of polymer conjugation on DNA compaction and particle formation. Structural analysis showed that chitosan-DNA conjugation is mainly via electrostatic interactions through polymer cationic charged NH2 and negatively charged backbone phosphate groups. As polymer size increases major DNA compaction and particle formation occurs. At high chitosan concentration major DNA structural changes observed indicating a partial B to A-DNA conformational transition.
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Affiliation(s)
- D Agudelo
- Department of Chemistry-Biochemistry and Physics, Université of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, Canada G9A 5H7
| | - L Kreplak
- Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie, University, Lord Dalhousie Drive, Halifax, NS, Canada B3H 4R2
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, Université of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, Canada G9A 5H7.
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41
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Structural modeling for DNA binding to antioxidants resveratrol, genistein and curcumin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 151:69-75. [DOI: 10.1016/j.jphotobiol.2015.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 01/07/2023]
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42
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Rubio-Magnieto J, Azene EG, Knoops J, Knippenberg S, Delcourt C, Thomas A, Richeter S, Mehdi A, Dubois P, Lazzaroni R, Beljonne D, Clément S, Surin M. Self-assembly and hybridization mechanisms of DNA with cationic polythiophene. SOFT MATTER 2015; 11:6460-6471. [PMID: 26179509 DOI: 10.1039/c5sm01484k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The combination of DNA and π-conjugated polyelectrolytes (CPEs) represents a promising approach to develop DNA hybridization biosensors, with potential applications for instance in the detection of DNA lesions and single-nucleotide polymorphisms. Here we exploit the remarkable optical properties of a cationic poly[3-(6'-(trimethylphosphonium)hexyl)thiophene-2,5-diyl] (CPT) to decipher the self-assembly of DNA and CPT. The ssDNA/CPT complexes have chiroptical signatures in the CPT absorption region that are strongly dependent on the DNA sequence, which we relate to differences in supramolecular interactions between the thiophene monomers and the various nucleobases. By studying DNA-DNA hybridization and melting processes on preformed ssDNA/CPT complexes, we observe sequence-dependent mechanisms that can yield DNA-condensed aggregates. Heating-cooling cycles show that non-equilibrium mixtures can form, noticeably depending on the working sequence of the hybridization experiment. These results are of high importance for the use of π-conjugated polyelectrolytes in DNA hybridization biosensors and in polyplexes.
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Affiliation(s)
- Jenifer Rubio-Magnieto
- Laboratory for Chemistry of Novel Materials, Center for Innovation in Materials and Polymers, University of Mons - UMONS, 20 Place du Parc, B-7000 Mons, Belgium.
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43
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Muenzner JK, Rehm T, Biersack B, Casini A, de Graaf IAM, Worawutputtapong P, Noor A, Kempe R, Brabec V, Kasparkova J, Schobert R. Adjusting the DNA Interaction and Anticancer Activity of Pt(II) N-Heterocyclic Carbene Complexes by Steric Shielding of the Trans Leaving Group. J Med Chem 2015; 58:6283-92. [DOI: 10.1021/acs.jmedchem.5b00896] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | - Angela Casini
- Department
of Pharmacokinetics, Toxicology and Targeting, Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Inge A. M. de Graaf
- Department
of Pharmacokinetics, Toxicology and Targeting, Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pawida Worawutputtapong
- Department
of Pharmacokinetics, Toxicology and Targeting, Research Institute
of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | | | - Viktor Brabec
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265 Brno, Czech Republic
| | - Jana Kasparkova
- Department
of Biophysics, Faculty of Science, Palacky University, 17. listopadu
12, CZ-77146 Olomouc, Czech Republic
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44
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Ostos F, Lebron J, Moyá M, Deasy M, López-Cornejo P. Binding of DNA by a dinitro-diester calix[4]arene: Denaturation and condensation of DNA. Colloids Surf B Biointerfaces 2015; 127:65-72. [DOI: 10.1016/j.colsurfb.2015.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/12/2014] [Accepted: 01/12/2015] [Indexed: 12/27/2022]
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45
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Brooks WH, Renaudineau Y. Epigenetics and autoimmune diseases: the X chromosome-nucleolus nexus. Front Genet 2015; 6:22. [PMID: 25763008 PMCID: PMC4329817 DOI: 10.3389/fgene.2015.00022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/16/2015] [Indexed: 12/18/2022] Open
Abstract
Autoimmune diseases occur more often in females, suggesting a key role for the X chromosome. X chromosome inactivation, a major epigenetic feature in female cells that provides dosage compensation of X-linked genes to avoid overexpression, presents special vulnerabilities that can contribute to the disease process. Disruption of X inactivation can result in loss of dosage compensation with expression from previously sequestered genes, imbalance of gene products, and altered endogenous material out of normal epigenetic context. In addition, the human X has significant differences compared to other species and these differences can contribute to the frequency and intensity of the autoimmune disease in humans as well as the types of autoantigens encountered. Here a link is demonstrated between autoimmune diseases, such as systemic lupus erythematosus, and the X chromosome by discussing cases in which typically non-autoimmune disorders complicated with X chromosome abnormalities also present lupus-like symptoms. The discussion is then extended to the reported spatial and temporal associations of the inactive X chromosome with the nucleolus. When frequent episodes of cellular stress occur, the inactive X chromosome may be disrupted and inadvertently become involved in the nucleolar stress response. Development of autoantigens, many of which are at least transiently components of the nucleolus, is then described. Polyamines, which aid in nucleoprotein complex assembly in the nucleolus, increase further during cell stress, and appear to have an important role in the autoimmune disease process. Autoantigenic endogenous material can potentially be stabilized by polyamines. This presents a new paradigm for autoimmune diseases: that many are antigen-driven and the autoantigens originate from altered endogenous material due to episodes of cellular stress that disrupt epigenetic control. This suggests that epigenetics and the X chromosome are important aspects of autoimmune diseases.
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Affiliation(s)
- Wesley H Brooks
- Department of Chemistry, University of South Florida Tampa, FL, USA
| | - Yves Renaudineau
- Research Unit INSERM ERI29/EA2216, SFR ScinBios, Labex Igo "Immunotherapy Graft, Oncology", Réseau Épigénétique et Réseau Canaux Ioniques du Cancéropole Grand Ouest, European University of Brittany Brest, France ; Laboratory of Immunology and Immunotherapy, Hôpital Morvan Brest, France
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46
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Prisecaru A, Molphy Z, Kipping RG, Peterson EJ, Qu Y, Kellett A, Farrell NP. The phosphate clamp: sequence selective nucleic acid binding profiles and conformational induction of endonuclease inhibition by cationic Triplatin complexes. Nucleic Acids Res 2014; 42:13474-87. [PMID: 25414347 PMCID: PMC4267626 DOI: 10.1093/nar/gku1157] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 01/27/2023] Open
Abstract
The substitution-inert polynuclear platinum(II) complex (PPC) series, [{trans-Pt(NH3)2(NH2(CH2)nNH3)}2-μ-(trans-Pt(NH3)2(NH2(CH2)nNH2)2}](NO3)8, where n = 5 (AH78P), 6 (AH78 TriplatinNC) and 7 (AH78H), are potent non-covalent DNA binding agents where nucleic acid recognition is achieved through use of the 'phosphate clamp' where the square-planar tetra-am(m)ine Pt(II) coordination units all form bidentate N-O-N complexes through hydrogen bonding with phosphate oxygens. The modular nature of PPC-DNA interactions results in high affinity for calf thymus DNA (Kapp ∼5 × 10(7) M(-1)). The phosphate clamp-DNA interactions result in condensation of superhelical and B-DNA, displacement of intercalated ethidium bromide and facilitate cooperative binding of Hoechst 33258 at the minor groove. The effect of linker chain length on DNA conformational changes was examined and the pentane-bridged complex, AH78P, was optimal for condensing DNA with results in the nanomolar region. Analysis of binding affinity and conformational changes for sequence-specific oligonucleotides by ITC, dialysis, ICP-MS, CD and 2D-(1)H NMR experiments indicate that two limiting modes of phosphate clamp binding can be distinguished through their conformational changes and strongly suggest that DNA condensation is driven by minor-groove spanning. Triplatin-DNA binding prevents endonuclease activity by type II restriction enzymes BamHI, EcoRI and SalI, and inhibition was confirmed through the development of an on-chip microfluidic protocol.
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Affiliation(s)
- Andreea Prisecaru
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ralph G. Kipping
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
| | - Erica J. Peterson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
| | - Yun Qu
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nicholas P. Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
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48
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Nakabayashi Y, Nakamura H, Kubota Y, Morimoto M, Kawasaki T, Nakai M, Yamauchi O. DNA interaction with dipolar ruthenium(II) ammine complexes containing 4,4′-bipyridinium as photochemotherapeutic agents. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.07.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Agudelo D, Bourassa P, Bérubé G, Tajmir-Riahi HA. Intercalation of antitumor drug doxorubicin and its analogue by DNA duplex: Structural features and biological implications. Int J Biol Macromol 2014; 66:144-50. [DOI: 10.1016/j.ijbiomac.2014.02.028] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 11/15/2022]
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50
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Malina J, Farrell NP, Brabec V. DNA Condensing Effects and Sequence Selectivity of DNA Binding of Antitumor Noncovalent Polynuclear Platinum Complexes. Inorg Chem 2014; 53:1662-71. [DOI: 10.1021/ic402796k] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jaroslav Malina
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.,
Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Nicholas P. Farrell
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Viktor Brabec
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, v.v.i.,
Kralovopolska 135, CZ-61265 Brno, Czech Republic
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