1
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Mudi A, Ray S, Bera M, Dolai M, Das M, Kundu P, Laha S, Choudhuri I, Chandra Samanta B, Bhattacharyya N, Maity T. A multi-spectroscopic and molecular docking approach for DNA/protein binding study and cell viability assay of first-time reported pendent azide bearing Cu(II)-quercetin and dicyanamide bearing Zn(II)-quercetin complexes. Heliyon 2023; 9:e22712. [PMID: 38125469 PMCID: PMC10731082 DOI: 10.1016/j.heliyon.2023.e22712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
In the current study, one new quercetin-based Zn(II) complex [Zn(Qr)(CNNCN)(H2O)2] (Complex 1) which is developed by condensation of quercetin with ZnCl2 in the presence of NaN(CN)2 and Cu(II) complex [Cu(Qr)N3(CH3OH)(H2O)] (complex 2) which is developed by the condensation reaction of quercetin and CuCl2 in presence of NaN3, are thoroughly examined in relation to their use in biomedicine. The results of several spectroscopic studied confirm the structure of both the complexes and the Density Functional Theory (DFT) study helps to optimize the structure of complex 1 and 2. After completion of the identification process, DNA and Human Serum Albumin (HSA) binding efficacy of both the investigated complexes are performed by implementing a long range of biophysical studies and a thorough analysis of the results unveils that complex 1 has better interaction efficacy with the macromolecules than complex 2. The binding efficacy of complex 1 is comparatively higher towards both macromolecules because of its pure groove binding mode during interaction with DNA and the presence of an extra H-bond during connection with HSA. The experimental host-guest binding results is fully validated by molecular docking study. Interestingly complex 1 shows better antioxidant properties than complex 2, as well as quercetin, and it has strong anticancer property with minimal damage to normal cells, which is proved by the MTT assay study. Better DNA and HSA binding efficacy of 1 may be the reason for the better anticancer property of complex 1.
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Affiliation(s)
- Anupam Mudi
- Department of Botany, Behala College, Behala, India
| | - Shubham Ray
- Department of Chemistry, Prabhat Kumar College, Contai, Contai, Purba Medinipur, 721404, India
| | - Manjushree Bera
- Department of Nutrition, Prabhat Kumar College, Contai, Contai, Purba Medinipur, 721404, India
| | - Malay Dolai
- Department of Chemistry, Prabhat Kumar College, Contai, Contai, Purba Medinipur, 721404, India
| | - Manik Das
- Department of Chemistry, Prabhat Kumar College, Contai, Contai, Purba Medinipur, 721404, India
| | - Pronab Kundu
- Department of Chemistry, Presidency University, Yelahanka, Bengaluru, 560064, India
| | | | | | | | | | - Tithi Maity
- Department of Chemistry, Prabhat Kumar College, Contai, Contai, Purba Medinipur, 721404, India
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2
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Metaphase Cells Enrichment for Efficient Use in the Dicentric Chromosome Assay. Cell Biochem Biophys 2022; 80:647-656. [PMID: 36216973 DOI: 10.1007/s12013-022-01106-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/03/2022]
Abstract
The dicentric chromosome assay (DCA), is considered the 'gold standard' for radiation biodosimetry. Yet, DCA, as currently implemented, may be impractical for emergency response applications, especially when time is of the essence, owing to its labor-intensive and time-consuming nature. The growth of a primary lymphocyte culture for 48 h in vitro is required for DCA, and manual scoring of dicentric chromosomes (DCs) requires an additional 24-48 h, resulting in an overall processing time of 72-96 h for dose estimation. In order to improve this timing. we introduce a protocol that will detect the metaphase cells in a population of cells, and then will harvest only those metaphase cells. Our metaphase enrichment approach is based on fixed human lymphocytes incubated with monoclonal, anti-phosphorylated H3 histone (ser 10). Antibodies against this histone have been shown to be specific for mitotic cells. Colcemid is used to arrest the mitotic cells in metaphase. Following that, a flow-cytometric sorting apparatus isolates the mitotic fraction from a large population of cells, in a few minutes. These mitotic cells are then spread onto a slide and treated with our C-Banding procedure [Gonen et al. 2022], to visualize the centromeres with DAPI. This reduces the chemical processing time to ~2 h. This reduces the time required for the DCA and makes it practical for a much wider set of applications, such as emergency response following exposure of a large population to ionizing radiation.
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3
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Supabowornsathit K, Faikhruea K, Ditmangklo B, Jaroenchuensiri T, Wongsuwan S, Junpra-Ob S, Choopara I, Palaga T, Aonbangkhen C, Somboonna N, Taechalertpaisarn J, Vilaivan T. Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids. Sci Rep 2022; 12:14250. [PMID: 35995925 PMCID: PMC9395382 DOI: 10.1038/s41598-022-18460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.
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Affiliation(s)
- Kotchakorn Supabowornsathit
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Theeranuch Jaroenchuensiri
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sutthida Wongsuwan
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sirikarn Junpra-Ob
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Chanat Aonbangkhen
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jaru Taechalertpaisarn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
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4
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Shurpik RV, Shurpik DN, Gerasimov AV, Stoikov II. Modification of Silicon Dioxide with Variously Substituted minothiacalix[4]arenes: Organic−Inorganic Nanoparticles or Nucleic Acid Binding. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022080103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Bisoi A, Sarkar S, Chandra Singh P. Contrasting Effect of Salts on the Binding of Antimalarial Drug Hydroxychloroquine with Different Sequences of Duplex DNA. J Phys Chem B 2022; 126:5605-5612. [PMID: 35867068 DOI: 10.1021/acs.jpcb.2c02755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxychloroquine (HCQ) is an important antimalarial drug which functions plausibly by targeting the DNA of parasites. Salts play a crucial role in the functionality of various biological processes. Hence, the effect of salts (NaCl and MgCl2) on the binding of HCQ with AT- and CG-DNAs as well as the binding-induced stability of both sequences of DNAs have been investigated using the spectroscopic and molecular dynamics (MD) simulation methods. It has been found that the effect of salts on the binding of HCQ is highly sensitive to the nature of ions as well as DNA sequences. The effect of ions is opposite for the binding of AT- and CG-DNAs as the presence of Mg2+ ions enhances the binding of HCQ with AT-DNA, whereas the binding of HCQ with CG-DNA gets decreased on the addition of both ions. Similarly, the presence of Mg2+ enhances the stabilization of HCQ-bound AT-DNA, whereas the effect is opposite for the CG-DNA in the presence of both the ions. The MD simulation study suggests that the hydration states of both ions are different and they interact differently in the minor and major grooves of both the sequences of DNA which may be one of the reasons for the different binding of HCQ with these two sequences of DNA in the presence of salts. The information about the effect of salts on the binding of HCQ with DNAs in a sequence-specific manner may be useful in understanding the mechanism of the action and toxicity effect of HCQ against malaria.
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Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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6
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Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. ACS NANO 2022; 16:8954-8966. [PMID: 35640255 PMCID: PMC9649841 DOI: 10.1021/acsnano.1c11575] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyun Min Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Jin X, Sun T, Wu Z, Wang D, Hu F, Xu J, Li X, Qiu J. Label-free hairpin probe for the rapid detection of Hg(II) based on T-Hg(II)-T. Anal Chim Acta 2022; 1221:340113. [DOI: 10.1016/j.aca.2022.340113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/11/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022]
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8
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An Optimized Method to Decellularize Human Trabecular Meshwork. Bioengineering (Basel) 2022; 9:bioengineering9050194. [PMID: 35621472 PMCID: PMC9137515 DOI: 10.3390/bioengineering9050194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Glaucoma is linked to raised intraocular pressure (IOP). The trabecular meshwork (TM) plays a major role in regulating IOP by enabling outflow of aqueous humor from the eye through its complex 3D structure. A lack of therapies targeting the dysfunctional TM highlights the need to develop biomimetic scaffolds that provide 3D in vitro models for glaucoma research or as implantable devices to regenerate TM tissue. To artificially mimic the TM’s structure, we assessed methods for its decellularization and outline an optimized protocol for cell removal and structural retention. Using bovine TM, we trialed 2 lysing agents—Trypsin (0.05% v/v) and Ammonium Hydroxide (NH4OH; 2% v/v). Twenty-four hours in Trypsin caused significant structural changes. Shorter exposure (2 h) reduced this disruption whilst decellularizing the tissue (dsDNA 26 ± 14 ng/mL (control 1970 ± 146 ng/mL)). In contrast, NH4OH lysed all cells (dsDNA 25 ± 21 ng/mL), and the TM structure remained intact. For human TM, 2% v/v NH4OH similarly removed cells (dsDNA 52 ± 4 ng/mL (control 1965 ± 233 ng/mL)), and light microscopy and SEM presented no structural damage. X-ray computed tomography enabled a novel 3D reconstruction of decellularized human TM and observation of the tissue’s intricate architecture. This study provides a new, validated method using NH4OH to decellularize delicate human TM without compromising tissue structure.
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9
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Oncocalyxone A (oncoA) has intrinsic fluorescence? Photodiagnosis Photodyn Ther 2022; 39:102869. [DOI: 10.1016/j.pdpdt.2022.102869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/19/2022]
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10
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A DAPI-Based Modified C-banding Technique for a Rapid Achieving High Photographic Contrast of Centromeres on Chromosomes. Cell Biochem Biophys 2022; 80:375-384. [PMID: 35137344 DOI: 10.1007/s12013-022-01065-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/25/2022] [Indexed: 11/27/2022]
Abstract
Many chromosome assays rely on the quantification of chromosome abnormalities in cells, and one important abnormality is the existence of more than one centromere for each chromosome. The quantification of such abnormalities has been studied before. However, this process is labor-intensive and time consuming. Thus, this assay is challenging for ex-laboratory applications, where speed is required. We present a visualization method that uses a cheap stain-DAPI, long (e.g., high-resolution) chromosomes and our modified C-banding method for labeling chromosomes. The labeled chromosomes can then be easily seen with a conventional and readily available fluorescence microscopy system. This method achieves an acceleration of the detection of the presence of constitutive heterochromatin in chromosomal centromeres by more than 10 times, to ~2 h, in Human lymphocyte cells and in cells of the human Jurkat line. This new procedure will ultimately provide an easier and cheaper alternative to FISH/PNA probes, or the classic Giemsa staining method. Simplification and reduction in time of the overall procedure will enable the utilization of centromere-counting assays in laboratory and ex-laboratory applications, including in emergency response.
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11
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Lee C, Kim YJ, Kim KS, Lee JY, Kim DN. Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules. Nucleic Acids Res 2021; 49:12591-12599. [PMID: 34850119 PMCID: PMC8643692 DOI: 10.1093/nar/gkab1119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Kyung Soo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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12
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Sarkar S, Roy S, Singh PC. Groove Switching of Hydroxychloroquine Modulates the Efficacy of Binding and Induced Stability to DNA. J Phys Chem B 2021; 125:6889-6896. [PMID: 34137627 DOI: 10.1021/acs.jpcb.1c03869] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxychloroquine (HCQ) is an important drug for the treatment of rheumatoid arthritis and malaria. HCQ targets specifically to nucleic acids for its action. However, the mechanism of HCQ binding and the effect of its binding on the stability of DNA are elusive. In this study, the binding mechanism of HCQ and the effect of binding on stability of different sequences of DNA have been investigated using spectroscopic and molecular dynamics (MD) simulation techniques. HCQ binds with all of the sequences of DNA and stabilizes them. However, binding efficacy of HCQ with DNA depends on its sequences as the binding constant is highest for pure guanine-cytosine (G-C) rich DNA and decreases with the increase of adenine-thymine (A-T) bases. HCQ prefers to interact with AT DNA through the minor groove whereas the major groove along with intercalation are the favorable binding mode in the case of GC DNA. The binding of HCQ in the major groove of GC DNA enhances the stacking between the bases compared to the case of AT DNA which leads to higher stability for GC DNA. It appears that the groove switching of HCQ is correlated with binding affinity as well as stability of different sequences of DNA.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sarita Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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13
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Sarkar S, Chandra Singh P. Spectroscopic and Simulation Studies of the Sequence-Dependent DNA Destabilization by a Fungicide. ACS OMEGA 2021; 6:14371-14378. [PMID: 34124459 PMCID: PMC8190899 DOI: 10.1021/acsomega.1c01228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/17/2021] [Indexed: 05/08/2023]
Abstract
The understanding of the structural change of DNA induced by fungicides is essential as the non-targeted action of fungicides causes genotoxicity, leading to several serious diseases such as cancer, behavioral change, and nausea. In this study, the binding of an important fungicide, namely, n-dodecylguanidine acetate (dodine), with B-DNA having different sequences of nucleobases and its effect on the structure of B-DNA has been investigated using spectroscopic and simulation methods. In general, the addition of dodine destabilizes DNA; however, the binding of dodine causing the destabilization of DNA is highly sequence dependent. In the case of adenine(A)-thymine(T)-based DNA, dodine intrudes into the minor groove of DNA and interacts with the A-T bases mainly through its hydrocarbon tail, which destabilizes the stacking interaction of the flanking bases. In contrast, the polar group of dodine interacts with guanine(G)-cytosine(C)-rich DNA, and the interaction is dynamic as it shuttles between the minor groove and terminal regions. The binding of dodine with G-C-rich DNA affects the stacking interaction of the terminal base regions specifically. This study reveals the base-specific binding mode of dodine, which causes destabilization of the duplex DNA.
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14
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Fantoni NZ, Brown T, Kellett A. DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology. Chembiochem 2021; 22:2184-2205. [PMID: 33570813 DOI: 10.1002/cbic.202000838] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/09/2021] [Indexed: 12/20/2022]
Abstract
DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex-nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site-specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex-nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence-specific targeting of these interactions can be achieved for gene engineering applications.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for, Cellular Biotechnology and Nano Research Facility, Dublin City University, Glasnevin, Dublin, 9, Ireland
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15
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Parameswaran P, Arora Y, Patidar R, Ranjan N. Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding. Biophys Chem 2021; 274:106589. [PMID: 33901777 DOI: 10.1016/j.bpc.2021.106589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
The bacterial A-site RNA is one of the key targets towards the development of new antibacterials including new treatment options for tuberculosis. Using DAPI as a prototype, we have explored the potential of bisamidines as a potential chemical motif for bacterial A-site recognition. We have demonstrated that the binding of DAPI shows a concentration-dependent thermal stabilization of the bacterial A-site RNA (ΔTm = 9.9 °C). The binding, however, does not show pH-dependent changes upon lowering of pH. Both UV-vis and CD experiments show that the DAPI binding involves base stacking with the RNA bases in a manner that is analogous to intercalation. Scatchard analysis of the UV-vis titration data revealed a micromolar affinity of the DAPI to the bacterial rRNA A-Site (Ka = 1.14 × 106 M-1) which was corroborated by the FID-based relative binding affinity comparison with aminoglycosides. The molecular docking studies showed binding poses consistent with polar and stacking interactions with the RNA. These studies highlight the role of amidines in bacterial A-site recognition and the need for the development of their structural analogs towards the making of aminoglycoside mimics.
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Affiliation(s)
- Preethi Parameswaran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India
| | - Yashaswina Arora
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India
| | - Rajesh Patidar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh 226002, India.
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16
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Sarkar S, Singh PC. Sequence specific hydrogen bond of DNA with denaturants affects its stability: Spectroscopic and simulation studies. Biochim Biophys Acta Gen Subj 2020; 1865:129735. [PMID: 32946929 DOI: 10.1016/j.bbagen.2020.129735] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/21/2020] [Accepted: 09/13/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Several different small molecules have been used to target the DNA helix in order to treat the diseases caused by its mutation. Guanidinium(Gdm+) and urea based drugs have been used for the diseases related to central nervous system, also as the anti-inflammatory and chemotherapeutic agent. However, the role of Gdm+ and urea in the stabilization/destabilization of DNA is not well understood. METHODS Spectroscopic techniques along with molecular dynamics (MD) simulation have been performed on different sequences of DNA in the presence of guanidinium chloride (GdmCl) and urea to decode the binding of denaturants with DNA and the role of hydrogen bond with the different regions of DNA in its stability/destability. RESULTS AND CONCLUSION Our study reveals that, Gdm+ of GdmCl and urea both intrudes into the groove region of DNA along with the interaction with its phosphate backbone. However, interaction of Gdm+ and urea with the nucleobases in the groove region is different. Gdm+ forms the intra-strand hydrogen bond with the central region of the both sequences of DNA whereas inter-strand hydrogen bond along with water assisted hydrogen bond takes place in the case of urea. The intra-strand hydrogen bond formation capability of Gdm+ with the nucleobases in the minor groove of DNA decreases its groove width which probably causes the stabilization of B-DNA in GdmCl. In contrast, the propensity of the formation of inter-strand hydrogen bond of urea with the nucleobases in the groove region of DNA without affecting the groove width destabilizes B-DNA as compared to GdmCl. This study depicts that the opposite effect of GdmCl and urea on the stability is a general property of B-DNA. However, the extent of stabilization/destabilization of DNA in Gdm+ and urea depend on its sequence probably due to the difference in the intra/inter-strand hydrogen bonding with different bases present in both the sequences of DNA. GENERAL SIGNIFICANCE The information obtained from this study will be useful for the designing of Gdm+ based drug molecule which can target the DNA more specifically and selectively.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 70032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 70032, India.
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17
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Velugula K, Kumar A, Chinta JP. Nuclease and anticancer activity of antioxidant conjugated terpyridine metal complexes. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Fudickar W, Linker T. Structural motives controlling the binding affinity of 9,10-bis(methylpyridinium)anthracenes towards DNA. Bioorg Med Chem 2020; 28:115432. [DOI: 10.1016/j.bmc.2020.115432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 10/24/2022]
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19
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Jung Y, Kim D. Nonviral Fluorescent Retrograde Tracers. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuna Jung
- Department of Biomedical Science, Graduate SchoolKyung Hee University Seoul 02447 Republic of Korea
| | - Dokyoung Kim
- Department of Biomedical Science, Graduate SchoolKyung Hee University Seoul 02447 Republic of Korea
- Department of Anatomy and Neurobiology, College of MedicineKyung Hee University Seoul 02447 Republic of Korea
- Center for Converging HumanitiesKyung Hee University Seoul 02447 Republic of Korea
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science InstituteKyung Hee University Seoul 02447 Republic of Korea
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20
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Application of Trifluoroacetic Acid as a Theranostic Agent for Chemical Ablation of Solid Tissue. J Vasc Interv Radiol 2019; 31:169-175. [PMID: 31537410 DOI: 10.1016/j.jvir.2019.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/01/2019] [Accepted: 05/07/2019] [Indexed: 11/21/2022] Open
Abstract
PURPOSE To evaluate trifluoroacetic acid (TFA) as a theranostic chemical ablation agent and determine the efficacy of TFA for both noninvasive imaging and tissue destruction. MATERIALS AND METHODS Fluorine-19 magnetic resonance imaging (19F-MRI) was optimized at 7 T using a custom-built volume coil. Fluorine images were acquired with both rapid acquisition with relaxation enhancement and balanced steady-state free precession (bSSFP) sequences with varying parameters to determine the optimal sequence for TFA. The theranostic efficacy of chemical ablation was examined by injecting TFA (100 μL; 0.25, 0.5, 1.0, and 2.0M) into ex vivo porcine liver. 19F and proton MRI were acquired and superimposed to visualize distribution of TFA in tissue and quantify sensitivity. Tissue damage was evaluated with gross examination, histology, and fluorescence microscopy. RESULTS The optimal 19F-MRI sequence was found to be bSSFP with a repetition time of 2.5 ms and flip angle of 70°. The minimum imageable TFA concentration was determined to be 6.7 ± 0.5 mM per minute of scan time (0.63×0.63×5.00 mm voxel), and real-time imaging (temporal resolution of at least 1 s-1) was achieved with 2M TFA both in vitro and in ex vivo tissue. TFA successfully coagulated tissue, and damage was locally confined. In addition to hepatic cord disruption, cytoskeletal collapse and chromatin clumping were observed in severely damaged areas in tissues treated with 0.5M or higher TFA concentrations. CONCLUSIONS TFA was determined to be a theranostic agent for chemical ablation of solid tissue. Ablation was both efficacious and imageable in ex vivo healthy tissue, even at low concentrations or with high temporal resolution.
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21
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Kimura E, Kikuta E. Macrocyclic Zinc(II) Complexes for Selective Recognition of Nucleobases in Single- and Double-Stranded Polynucleotides. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967400103165119] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The model study of zinc enzyme by Zn2+–cyclen complexes (cyclen = 1, 4, 7, 10-tetraazacyclododecane) disclosed the intrinsic properties of zinc(II) as having strong anion affinities and yet the resulting Zn2+–anion bonds have a labile nature. The basic understanding has evolved into novel selective nucleobase recognition by the Zn2+–cyclen complexes. The Zn2+–aromatic pendant cyclen complexes selectively and effectively bind to thymine T (or uracil U) in single- and double-stranded DNA (or RNA). The Zn2+ complexes work like molecular zippers to break A–T pairs in double-stranded DNA, as proven by various physicochemical and DNA footprinting measurements. Moreover, these Zn2+–complexes affect relevant biochemical and ultimately biological properties such as inhibition of a transcriptional factor and antimicrobial activities.
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Affiliation(s)
- Eiichi Kimura
- Department of Medicinal Chemistry, Faculty of Medicine, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Emiko Kikuta
- Department of Medicinal Chemistry, Faculty of Medicine, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
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22
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Carter EK, Laughlin-Toth S, Dodd T, Wilson WD, Ivanov I. Small molecule binders recognize DNA microstructural variations via an induced fit mechanism. Phys Chem Chem Phys 2019; 21:1841-1851. [PMID: 30629058 PMCID: PMC6497476 DOI: 10.1039/c8cp05537h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Regulation of gene-expression by specific targeting of protein-nucleic acid interactions has been a long-standing goal in medicinal chemistry. Transcription factors are considered "undruggable" because they lack binding sites well suited for binding small-molecules. In order to overcome this obstacle, we are interested in designing small molecules that bind to the corresponding promoter sequences and either prevent or modulate transcription factor association via an allosteric mechanism. To achieve this, we must design small molecules that are both sequence-specific and able to target G/C base pair sites. A thorough understanding of the relationship between binding affinity and the structural aspects of the small molecule-DNA complex would greatly aid in rational design of such compounds. Here we present a comprehensive analysis of sequence-specific DNA association of a synthetic minor groove binder using long timescale molecular dynamics. We show how binding selectivity arises from a combination of structural factors. Our results provide a framework for the rational design and optimization of synthetic small molecules in order to improve site-specific targeting of DNA for therapeutic uses in the design of selective DNA binders targeting transcription regulation.
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Affiliation(s)
- E. Kathleen Carter
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA. ;
| | - Sarah Laughlin-Toth
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA. ;
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas Dodd
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA. ;
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA. ;
| | - Ivaylo Ivanov
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA. ;
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23
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Li C, Takahashi T, Shrestha T, Kinoshita E, Matsubara T, Matsumoto M, Maruyama H. 4',6-Diamidino-2-Phenylindole Distinctly Labels Tau Deposits. J Histochem Cytochem 2018; 66:737-751. [PMID: 30106598 DOI: 10.1369/0022155418793600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tau deposits have distinct biochemical characteristics and vary morphologically based on identification with tau antibodies and several chemical dyes. Here, we report 4',6-diamidino-2-phenylindole (DAPI)-positivity of tau deposits. Furthermore, we investigated the cause for this positivity. DAPI was positive in 3R/4R (3-repeat/4-repeat) tau deposits in Alzheimer's disease, myotonic dystrophy, and neurodegeneration with brain iron accumulation, and in 4R tau deposits in corticobasal degeneration, but negative in 4R tau deposits in frontotemporal dementia with parkinsonism-17 and progressive supranuclear palsy. The peak emission wavelength of DAPI after binding to a tau deposit was similar to that after binding to a nucleus. This DAPI-positivity was conspicuous at the optimum concentration of 2 μg/ml. DAPI-positivity was diminished after formic acid treatment, but preserved after nucleic acid elimination and phosphate moiety blocking. Our results suggest that staining with 2 μg/ml DAPI is a common but useful tool to differentially detect tau deposits in various tauopathies.
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Affiliation(s)
- Chengyu Li
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tetsuya Takahashi
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tejashwi Shrestha
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Eiji Kinoshita
- Department of Functional Molecular Science, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoyasu Matsubara
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Masayasu Matsumoto
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan.,Sakai City Medical Center, Sakai, Japan
| | - Hirofumi Maruyama
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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24
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Park CK, Hong SK, Kim YH, Cho H. Nucleic Acid-Binding Fluorochromes and Nanoparticles: Structural Aspects of Binding Affinity and Fluorescence Intensity. Macromol Res 2018. [DOI: 10.1007/s13233-018-6053-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Ali MS, Farah MA, Al-Lohedan HA, Al-Anazi KM. Comprehensive exploration of the anticancer activities of procaine and its binding with calf thymus DNA: a multi spectroscopic and molecular modelling study. RSC Adv 2018; 8:9083-9093. [PMID: 35541873 PMCID: PMC9078652 DOI: 10.1039/c7ra13647a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/21/2018] [Indexed: 11/21/2022] Open
Abstract
DNA demethylating agent procaine binds at the minor groove of ct-DNA and increases the anticancer activity of doxorubicin.
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Affiliation(s)
- Mohd. Sajid Ali
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh-11451
- Saudi Arabia
| | - Mohammad Abul Farah
- Department of Zoology
- College of Science
- King Saud University
- Riyadh-11451
- Saudi Arabia
| | - Hamad A. Al-Lohedan
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh-11451
- Saudi Arabia
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26
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Holmgaard List N, Knoops J, Rubio-Magnieto J, Idé J, Beljonne D, Norman P, Surin M, Linares M. Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder. J Am Chem Soc 2017; 139:14947-14953. [DOI: 10.1021/jacs.7b05994] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nanna Holmgaard List
- School of Biotechnology, Division of Theoretical Chemistry & Biology, KTH Royal Institute of Technology, Roslagstullsbacken 15, 114 21 Stockholm, Sweden
| | - Jérémie Knoops
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Jenifer Rubio-Magnieto
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Julien Idé
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - David Beljonne
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Patrick Norman
- School of Biotechnology, Division of Theoretical Chemistry & Biology, KTH Royal Institute of Technology, Roslagstullsbacken 15, 114 21 Stockholm, Sweden
| | - Mathieu Surin
- Laboratory
for Chemistry of Novel Materials, Center for Innovation and Research
in Materials and Polymers, University of Mons−UMONS, Place
du Parc, 20, 7000 Mons, Belgium
| | - Mathieu Linares
- School of Biotechnology, Division of Theoretical Chemistry & Biology, KTH Royal Institute of Technology, Roslagstullsbacken 15, 114 21 Stockholm, Sweden
- Swedish
e-Science Research Centre, KTH Royal Institute of Technology, 104 50 Stockholm, Sweden
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27
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Farahat AA, Kumar A, Say M, Wenzler T, Brun R, Paul A, Wilson WD, Boykin DW. Exploration of DAPI analogues: Synthesis, antitrypanosomal activity, DNA binding and fluorescence properties. Eur J Med Chem 2017; 128:70-78. [PMID: 28152428 PMCID: PMC5341734 DOI: 10.1016/j.ejmech.2017.01.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 02/05/2023]
Abstract
The DAPI structure has been modified by replacing the phenyl group with substituted phenyl or heteroaryl rings. Twelve amidines were synthesized and their DNA binding, fluorescence properties, in vitro and in vivo activities were evaluated. These compounds are shown to bind in the DNA minor groove with high affinity, and exhibit superior in vitro antitrypanosomal activity to that of DAPI. Six new diamidines (5b, 5c, 5d, 5e, 5f and 5j) exhibit superior in vivo activity to that of DAPI and four of these compounds provide 100% animal cure at a low dose of 4 × 5 mg/kg i.p. in T. b. rhodesiense infected mice. Generally, the fluorescence properties of the new analogues are inferior to that of DAPI with the exception of compound 5i which shows a moderate increase in efficacy while compound 5k is comparable to DAPI.
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Affiliation(s)
- Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Martial Say
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Tanja Wenzler
- Swiss Tropical and Public Health Institute, Basel 4002, Switzerland; University of Basel, Basel, 4003, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Basel 4002, Switzerland; University of Basel, Basel, 4003, Switzerland
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
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28
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Reis LA, Rocha MS. DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes. Biopolymers 2017; 107. [DOI: 10.1002/bip.23015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 01/10/2023]
Affiliation(s)
- L. A. Reis
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
| | - M. S. Rocha
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
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29
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Chaires JB. A small molecule--DNA binding landscape. Biopolymers 2016; 103:473-9. [PMID: 25913470 DOI: 10.1002/bip.22660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/16/2015] [Indexed: 02/03/2023]
Abstract
This brief account traces the development of a "competition dialysis" method used to characterize the structural and sequence selectivity of DNA binding compounds. The method was inspired by a simple "differential dialysis" method pioneered by Don Crothers to explore base-selective intercalator binding. Results from compiled competition dialysis studies provide a small-molecule DNA binding landscape that shows a rich diversity of interactions and molecular recognition.
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Affiliation(s)
- Jonathan B Chaires
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
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30
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Gao C, Liu SY, Zhang X, Liu YK, Qiao CD, Liu ZE. Two-photon fluorescence and fluorescence imaging of two styryl heterocyclic dyes combined with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 156:1-8. [PMID: 26629954 DOI: 10.1016/j.saa.2015.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 06/05/2023]
Abstract
Two new styryl heterocyclic two-photon (TP) materials, 4-[4-(N-methyl)styrene]-imidazo [4,5-f][1,10] phenanthroline-benzene iodated salt (probe-1) and 4,4-[4-(N-methyl)styrene]-benzene iodated salt (probe-2) were successfully synthesized and studied as potential fluorescent probes of DNA detection. The linear and nonlinear photophysical properties of two compounds in different solvents were investigated. The absorption, one- and two-photon fluorescent spectra of the free dye and dye-DNA complex were also examined to evaluate their photophysical properties. The binding constants of dye-DNA were obtained according to Scatchard equation with good values. The results showed that two probes could be used as fluorescent DNA probes by two-photon excitation, and TP fluorescent properties of probe-1 are superior to that of probe-2. The fluorescent method date indicated that the mechanisms of dye-DNA complex interaction may be groove binding for probe-1 and electrostatic interaction for probe-2, respectively. The MTT assay experiments showed two probes are low toxicity. Moreover, the TP fluorescence imaging of DNA detection in living cells at 800 nm indicated that the ability to locate in cell nuclei of probe-1 is better than that of probe-2.
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Affiliation(s)
- Chao Gao
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Shu-yao Liu
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Xian Zhang
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China.
| | - Ying-kai Liu
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Cong-de Qiao
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Zhao-e Liu
- Qilu Hospital of Shandong University, Jinan 250012, China
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31
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Slator C, Barron N, Howe O, Kellett A. [Cu(o-phthalate)(phenanthroline)] Exhibits Unique Superoxide-Mediated NCI-60 Chemotherapeutic Action through Genomic DNA Damage and Mitochondrial Dysfunction. ACS Chem Biol 2016; 11:159-71. [PMID: 26488846 DOI: 10.1021/acschembio.5b00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The in cellulo catalytic production of reactive oxygen species (ROS) by copper(II) and iron(II) complexes is now recognized as a major mechanistic model in the design of effective cytotoxins of human cancer. The developmental complex, [Cu(o-phthalate)(1,10-phenanthroline)] (Cu-Ph), was recently reported as an intracellular ROS-active cytotoxic agent that induces double strand breaks in the genome of human cancer cells. In this work, we report the broad-spectrum action of Cu-Ph within the National Cancer Institute's (NCI) Developmental Therapeutics Program (DTP), 60 human cancer cell line screen. The activity profile is compared to established clinical agents-via the COMPARE algorithm-and reveals a novel mode of action to existing metal-based therapeutics. In this study, we identify the mechanistic activity of Cu-Ph through a series of molecular biological studies that are compared directly to the clinical DNA intercalator and topoisomerase II poison doxorubicin. The presence of ROS-specific scavengers was employed for in vitro and intracellular evaluation of prevailing radical species responsible for DNA oxidation with superoxide identified as playing a critical role in this mechanism. The ROS targeting properties of Cu-Ph on mitochondrial membrane potential were investigated, which showed that it had comparable activity to the uncoupling ionophore, carbonyl cyanide m-chlorophenyl hydrazine. The induction and origins of apoptotic activation were probed through detection of Annexin V and the activation of initiator (8,9) and executioner caspases (3/7) and were structurally visualized using confocal microscopy. Results here confirm a unique radical-induced mechanistic profile with intracellular hallmarks of damage to both genomic DNA and mitochondria.
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Affiliation(s)
- Creina Slator
- School
of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Niall Barron
- School
of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Orla Howe
- School of Biological Sciences & Focas Research Institute, Dublin Institute of Technology, Camden Row, Dublin 8, Ireland
| | - 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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Patra A, Hazra S, Samanta N, Suresh Kumar G, Mitra RK. Micelle induced dissociation of DNA–ligand complexes: The effect of ligand binding specificity. Int J Biol Macromol 2016; 82:418-24. [DOI: 10.1016/j.ijbiomac.2015.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/19/2015] [Accepted: 11/05/2015] [Indexed: 11/16/2022]
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Abstract
Good preparations are essential for informative analysis of both somatic and meiotic chromosomes, cytogenetics, and cell divisions. Fluorescent chromosome staining allows even small chromosomes to be visualized and counted, showing their morphology. Aneuploidies and polyploidies can be established for species, populations, or individuals while changes occurring in breeding lines during hybridization or tissue culture and transformation protocols can be assessed. The process of division can be followed during mitosis and meiosis including pairing and chiasma distribution, as well as DNA organization and structure during the evolution of chromosomes can be studied. This chapter presents protocols for pretreatment and fixation of material, including tips of how to grow plants to get good and healthy meristem with many divisions. The chromosome preparation technique is described using proteolytic enzymes, but acids can be used instead. Chromosome slide preparations are suitable for fluorochrome staining for fast screening (described in the chapter) or fluorescent in situ hybridization (see Schwarzacher and Heslop-Harrison, In situ hybridization. BIOS Scientific Publishers, Oxford, 2000).
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Affiliation(s)
- Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Linhoff MW, Garg SK, Mandel G. A high-resolution imaging approach to investigate chromatin architecture in complex tissues. Cell 2015; 163:246-55. [PMID: 26406379 DOI: 10.1016/j.cell.2015.09.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 05/22/2015] [Accepted: 08/11/2015] [Indexed: 01/08/2023]
Abstract
We present ChromATin, a quantitative high-resolution imaging approach for investigating chromatin organization in complex tissues. This method combines analysis of epigenetic modifications by immunostaining, localization of specific DNA sequences by FISH, and high-resolution segregation of nuclear compartments using array tomography (AT) imaging. We then apply this approach to examine how the genome is organized in the mammalian brain using female Rett syndrome mice, which are a mosaic of normal and Mecp2-null cells. Side-by-side comparisons within the same field reveal distinct heterochromatin territories in wild-type neurons that are altered in Mecp2-null nuclei. Mutant neurons exhibit increased chromatin compaction and a striking redistribution of the H4K20me3 histone modification into pericentromeric heterochromatin, a territory occupied normally by MeCP2. These events are not observed in every neuronal cell type, highlighting ChromATin as a powerful in situ method for examining cell-type-specific differences in chromatin architecture in complex tissues.
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Affiliation(s)
- Michael W Linhoff
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Saurabh K Garg
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Gail Mandel
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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35
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Stefanucci A, Mosquera J, Vázquez E, Mascareñas JL, Novellino E, Mollica A. Synthesis, Characterization, and DNA Binding Profile of a Macrocyclic β-Sheet Analogue of ARC Protein. ACS Med Chem Lett 2015; 6:1220-4. [PMID: 26713108 DOI: 10.1021/acsmedchemlett.5b00363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/29/2015] [Indexed: 12/29/2022] Open
Abstract
ARC repressor (apoptosis repressor with caspase recruitment domain) is a protein which binds selectively to a specific sequence of DNA. In humans, ARC is primarily expressed in striated muscle tissue, which normally does not undergo rapid cell turnover. This suggests that ARC may play a protective role in the prevention against Duchenne Muscular Dystrophy and several types of tumors. In this Letter we report the synthesis, characterization, and conformational analysis of a β-sheet ARC repressor mimetic, based on the amino acid sequence of the β-sheet domain in the ARC protein. The ability of this β-sheet macrocycle to bind to double-stranded DNA was also evaluated using spectroscopic methods. Our data show that the synthetic peptide has a defined conformation and is able to bind DNA with reasonable affinity. These initial results lay the groundwork for the design of novel β-sheets folded peptides as valuable substitutes of transcription factor proteins in drug therapy.
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Affiliation(s)
- Azzurra Stefanucci
- Dipartimento
di Chimica, Sapienza, Università di Roma, P.le A. Moro
5, 00187 Rome, Italy
| | - Jesús Mosquera
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Eugènio Vázquez
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - José L. Mascareñas
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy
| | - Adriano Mollica
- Dipartimento
di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
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36
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A label-free fluorescence turn-on sensor for rapid detection of cysteine. Talanta 2015; 138:144-148. [DOI: 10.1016/j.talanta.2015.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 11/18/2022]
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37
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Verma SD, Pal N, Singh MK, Sen S. Sequence-Dependent Solvation Dynamics of Minor-Groove Bound Ligand Inside Duplex-DNA. J Phys Chem B 2015; 119:11019-29. [DOI: 10.1021/acs.jpcb.5b01977] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sachin Dev Verma
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nibedita Pal
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Moirangthem Kiran Singh
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory,
School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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38
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Biological potential of carbazole derivatives. Eur J Med Chem 2015; 94:405-26. [DOI: 10.1016/j.ejmech.2015.02.059] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 02/19/2015] [Accepted: 02/28/2015] [Indexed: 11/21/2022]
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39
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Montalvo-Quirós S, Taladriz-Sender A, Kaiser M, Dardonville C. Antiprotozoal activity and DNA binding of dicationic acridones. J Med Chem 2015; 58:1940-9. [PMID: 25642604 DOI: 10.1021/jm5018303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dicationic acridone derivatives were synthesized and their antiparasitic activity was evaluated. Acridones displayed in vitro nanomolar IC50 values against Trypanosoma brucei rhodesiense STIB900 with selectivity indices >1000. Compounds 1b, 3a, and 3b were as potent as the reference drug melarsoprol in this assay. Submicromolar-range activities were observed against wild-type (NF54) and resistant (K1) strains of Plasmodium falciparum, whereas no significant activity was detected against Trypanosoma cruzi or Leishmania donovani. Compounds 1a and 1b were curative in the STIB900 mouse model for human African trypanosomiasis. UV spectrophotometric titrations and circular dichroism (CD) experiments with fish sperm (FS) DNA showed that these compounds form complexes with DNA with binding affinities in the 10(4) M(-1) range. Biological and biophysical data show that antiparasitic activity, toxicity, and DNA binding of this series of acridones are dependent on the relative position of both imidazolinium cations on the heterocyclic scaffold.
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Affiliation(s)
- Sandra Montalvo-Quirós
- Instituto de Química Médica, Consejo Superior de Investigaciones Científicas (IQM-CSIC) , Juan de la Cierva 3, E-28006 Madrid, Spain
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40
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Kumari R, Bhowmick S, Das N, Das P. Binding and interaction of di- and tri-substituted organometallic triptycene palladium complexes with DNA. J Biol Inorg Chem 2014; 19:1221-32. [DOI: 10.1007/s00775-014-1180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/13/2014] [Indexed: 01/08/2023]
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41
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Reis LA, Ramos EB, Rocha MS. DNA Interaction with Diaminobenzidine Studied with Optical Tweezers and Dynamic Light Scattering. J Phys Chem B 2013; 117:14345-50. [DOI: 10.1021/jp409544e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. A. Reis
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E. B. Ramos
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M. S. Rocha
- Laboratório de Física
Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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42
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Biancardi A, Biver T, Secco F, Mennucci B. An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools. Phys Chem Chem Phys 2013; 15:4596-603. [PMID: 23423468 DOI: 10.1039/c3cp44058c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.
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Affiliation(s)
- Alessandro Biancardi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento, 35-56126 Pisa, Italy.
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43
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Zhao C, Zhang Y, Wang X, Cao J. Development of BODIPY-based fluorescent DNA intercalating probes. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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44
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Wang G, Yan C, Lu Y. Exploring DNA binding properties and biological activities of dihydropyrimidinones derivatives. Colloids Surf B Biointerfaces 2013; 106:28-36. [DOI: 10.1016/j.colsurfb.2013.01.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 01/10/2013] [Indexed: 11/29/2022]
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45
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Ando M, Kamei R, Komagoe K, Inoue T, Yamada K, Katsu T. In situ potentiometric method to evaluate bacterial outer membrane-permeabilizing ability of drugs: example using antiprotozoal diamidines. J Microbiol Methods 2012; 91:497-500. [PMID: 23046554 DOI: 10.1016/j.mimet.2012.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/25/2012] [Accepted: 09/29/2012] [Indexed: 10/27/2022]
Abstract
We introduced a new assay system, combining tyrocidine A and a K(+)-selective electrode, to evaluate the bacterial outer membrane-permeabilizing ability of drugs. Tyrocidine A, in the presence of an outer membrane permeabilizer, increased the permeability to K(+) of the cytoplasmic membrane of Escherichia coli, because this antibiotic could markedly increase the permeability of phospholipid layers constituting the cytoplasmic membrane, while it acted weakly on the outer membrane. Hence, the novel function of agents increasing the permeability of the outer membrane could be examined directly by monitoring the tyrocidine A-induced leakage of K(+) from the bacterial cytoplasm using a K(+)-selective electrode. We found that antiprotozoal diamidines, such as diminazene, pentamidine, and 4',6-diamidino-2-phenylindole (DAPI), can increase the permeability of the bacterial outer membrane and appropriate lipophilicity is important for diamidines to permeabilize the outer membrane.
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Affiliation(s)
- Makoto Ando
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Kita, Okayama, Japan
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46
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Johnson RP, Richardson JA, Brown T, Bartlett PN. A label-free, electrochemical SERS-based assay for detection of DNA hybridization and discrimination of mutations. J Am Chem Soc 2012; 134:14099-107. [PMID: 22835041 DOI: 10.1021/ja304663t] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A label-free, surface-enhanced Raman spectroscopy-based assay for detecting DNA hybridization at an electrode surface and for distinguishing between mutations in DNA is demonstrated. Surface-immobilized DNA is exposed to a binding agent that is selective for dsDNA and acts as a reporter molecule. Upon application of a negative potential, the dsDNA denatures into its constituent strands, and the changes in the spectra of the reporter molecule are monitored. This method has been used to distinguish between a wild-type, 1653C/T single-point mutation and ΔF508 triplet deletion in the CFTR gene. The use of dsDNA-selective binding agents as reporter molecules in a discrimination assay removes the burden of synthetically modifying the target to be detected, while retaining flexibility in the choice of the reporter molecule.
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Affiliation(s)
- Robert P Johnson
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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47
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Sánchez MI, Martínez-Costas J, Gonzalez F, Bermudez MA, Vázquez ME, Mascareñas JL. In vivo light-driven DNA binding and cellular uptake of nucleic acid stains. ACS Chem Biol 2012; 7:1276-80. [PMID: 22550994 DOI: 10.1021/cb300100r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chemical derivatization of nucleic stains such as ethidium bromide or DAPI with tailored, photoresponsive caging groups, allows for "on demand" spatiotemporal control of their in vivo nucleic acid binding, as well as for improving their cellular uptake. This effect was particularly noteworthy for a nitro-veratryloxycarbonyl-caged derivative of ethidium bromide that, in contrast with the parent stain, is effectively internalized into living cells. The activation strategy works in light-accessible, therapeutically relevant settings, such as human retinas, and can even be applied for the release of active compounds in the eyes of living mice.
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Affiliation(s)
| | | | - Francisco Gonzalez
- Departamento de Fisiología, Universidad de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
- Servicio
de Oftalmología, Complejo Hospitalario Universitario de Santiago de Compostela, 15706 Santiago de Compostela,
Spain
| | - María A. Bermudez
- Departamento de Fisiología, Universidad de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
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48
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Bordello J, Sánchez MI, Vázquez ME, Mascareñas JL, Al-Soufi W, Novo M. Single-Molecule Approach to DNA Minor-Groove Association Dynamics. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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49
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Bordello J, Sánchez MI, Vázquez ME, Mascareñas JL, Al-Soufi W, Novo M. Single-molecule approach to DNA minor-groove association dynamics. Angew Chem Int Ed Engl 2012; 51:7541-4. [PMID: 22700034 DOI: 10.1002/anie.201201099] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/26/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Jorge Bordello
- Departamento de Química Física, Universidade de Santiago de Compostela, Facultade de Ciencias, 27001 Lugo, Spain
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50
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Hepel M, Stobiecka M, Peachey J, Miller J. Intervention of glutathione in pre-mutagenic catechol-mediated DNA damage in the presence of copper(II) ions. Mutat Res 2012; 735:1-11. [PMID: 22683503 DOI: 10.1016/j.mrfmmm.2012.05.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 05/25/2012] [Accepted: 05/29/2012] [Indexed: 11/28/2022]
Abstract
The catechol-mediated DNA damage in the presence of Cu(II) ions involves oxidation of guanine to 8-oxoguanine (8-oxoG) and DNA strand scission. It proceeds through the reactive oxygen species (ROS) generation. The mutagenicity of 8-oxoG lesions is due to its miscoding propensity reflected in GC→TA transversion taking place during the DNA repair process. To gain new insights into the nature of catechol-mediated DNA damage and its prevention, we have investigated the changes in DNA melting characteristics and 8-oxoG formation as the indicators of DNA damage in a model calf-thymus DNA system. A novel fluorescence method for DNA melting temperature determination, based on DAPI fluorescent-probe staining, has been proposed. The DNA melting-onset temperature has been found to be more sensitive to DNA damage than the standard melting temperature due to the increased width of the melting transition observed in oxidatively damaged DNA. We have found that the efficiency of Fenton cascade in generating DNA-damaging ROS is higher for catechol than for GSH, two strong antioxidants, mainly due to the much longer distance between ROS-generating radical group in GS to nucleobases than that of semiquinone radical group to nucleobases (2.1nm vs. 0.27nm), making the ROS transport from GSH an order of magnitude less likely to damage DNA because of short lifetime of HO radicals. The antioxidant and DNA-protecting behaviors of GSH have been elucidated. We have found that the redox potential of GSH/GSSG couple is lower than that of catechol/semiquinone couple. Hence, GSH keeps catechol in the reduced state, thereby shutting down the initial step of the catechol-mediated Fenton cascade. The catechol-induced DNA damage in the presence of Cu(II) ions has also been confirmed in studies of ON-OFF hairpin-oligonucleotide beacons.
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Affiliation(s)
- Maria Hepel
- Department of Chemistry, State University of New York at Potsdam, Potsdam, NY 13676, United States.
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