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Xie C, Chen Z, Chen K, Hu Y, Xu F, Pan L. Diverse Chiral Nanotubes Assembled from Identical DNA Strands. NANO LETTERS 2024. [PMID: 38967319 DOI: 10.1021/acs.nanolett.4c02071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
DNA nanotubes with controllable geometries hold a wide range of interdisciplinary applications. When preparing DNA nanotubes of varying widths or distinct chirality, existing methods require repeatedly designing and synthesizing specific DNA sequences, which can be costly and laborious. Here, we proposed an intercalator-assisted DNA tile assembly method which enables the production of DNA nanotubes of diverse widths and chirality using identical DNA strands. Through adjusting the concentration of intercalators during assembly, the twisting direction and extent of DNA tiles could be modulated, leading to the formation of DNA nanotubes featuring controllable widths and chirality. Moreover, through introducing additional intercalators and secondary annealing, right-handed nanotubes could be reconfigured into distinct left-handed nanotubes. We expect that this method could be universally applied to modulating the self-assembly pathways of various DNA tiles and other chiral materials, advancing the landscape of DNA tile assembly.
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Affiliation(s)
- Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043 Hebei, China
| | - Fei Xu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
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2
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Khan HY, Ansari MF, Tabassum S, Arjmand F. A review on the recent advances of interaction studies of anticancer metal-based drugs with therapeutic targets, DNA and RNAs. Drug Discov Today 2024; 29:104055. [PMID: 38852835 DOI: 10.1016/j.drudis.2024.104055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/18/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024]
Abstract
Metal-based drugs hold promise as potent anticancer agents owing to their unique interactions with cellular targets. This review discusses recent advances in our understanding of the intricate molecular interactions of metal-based anticancer compounds with specific therapeutic targets in cancer cells. Advanced computational and experimental methodologies delineate the binding mechanisms, structural dynamics and functional outcomes of these interactions. In addition, the review sheds light on the precise modes of action of these drugs, their efficacy and the potential avenues for further optimization in cancer-treatment strategies and the development of targeted and effective metal-based therapies for combating various forms of cancer.
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Affiliation(s)
- Huzaifa Yasir Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | | | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India.
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3
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Dutra JL, Honorato J, Graminha A, Moraes CAF, de Oliveira KT, Cominetti MR, Castellano EE, Batista AA. Pd(II)/diphosphine/curcumin complexes as potential anticancer agents. Dalton Trans 2024. [PMID: 38938129 DOI: 10.1039/d4dt01045k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Palladium(II) complexes have stimulated research interest mainly due to their in vitro cytotoxicity against various cancer cell lines and their low cytotoxicity in healthy cells. Thus, in this work, we combined Pd(II)/phosphine systems with the natural product curcumin as a ligand, obtaining a series of complexes, [Pd(cur)(PPh3)2]PF6 (A1), [Pd(cur)(dppe)]PF6 (A2), [Pd(cur)(dppp)]PF6 (A3), [Pd(cur)(dppb)]PF6 (A4) and [Pd(cur)(dppf)]PF6 (A5), where dppe = 1,2-bis(diphenylphosphino)ethane, dppp = 1,3-bis(diphenylphosphino)propane, dppb = 1,4-bis(diphenylphosphino)butane, and dppf = 1,1'-bis(diphenylphosphino)ferrocene (P-P), which were characterized by elemental analysis, molar conductivity analysis, and mass, NMR (1H, 13C, 31P{1H}), UV-vis, and IR spectroscopies, and four of them (A1, A2, A4, and A5) by X-ray crystallography. The in vitro cell viability of the complexes A1-A5, cisplatin, and the free ligand curcumin against MDA-MB-231 (human triple-negative breast tumor cells), SK-BR-3 (human breast tumor cells), A549 (human lung tumor cells), MRC-5 (non-tumor human lung cells), A2780 (human ovarian carcinoma cells), and A2780cis (cisplatin-resistant human ovarian carcinoma cells), was evaluated by the MTT colorimetric assay. For the tumor cell lines tested, the complexes showed good anticancer activities. The results showed that in general the complexes had lower IC50 values than free curcumin and the precursors [PdCl2(P-P)]. IC50 results obtained for the A1-A5 complexes, in the MCF-7 cell line, are similar to those that had already been observed for some Pd/bipy/curcumin complexes. In the MDA-MB-231 cell line, complexes A1 and A5 stood out, with their lowest IC50 values, around 5 μmol L-1, and the complexes appeared to be more active (lower IC50 values) against the ovarian cell lines. Complex A1 was 23 and 22-fold more cytotoxic than cisplatin, against the A2780 and A2780cis cells, respectively. The complex A1 was studied on A2780cis cells and it was found that this complex inhibits colony formation and induces cell cycle arrest in the sub-G1 phase in a concentration-dependent manner and leads to cell death by apoptosis. The DCFDA assay revealed a potent ROS induction for complex A1.
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Affiliation(s)
- Jocely L Dutra
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, CP 676, CEP 13561-901, São Carlos, SP, Brazil.
- Departamento de Química, Universidade Federal do Amazonas - UFAM, CEP 69077-000, Itacoatiara, AM, Brazil
| | - João Honorato
- Instituto de Química, Universidade de São Paulo - USP, CEP 05508-900, São Paulo, SP, Brazil
| | - Angélica Graminha
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, CP 676, CEP 13561-901, São Carlos, SP, Brazil.
| | - Carlos André F Moraes
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, CP 676, CEP 13561-901, São Carlos, SP, Brazil.
| | - Kleber T de Oliveira
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, CP 676, CEP 13561-901, São Carlos, SP, Brazil.
| | - Marcia R Cominetti
- Departamento de Gerontologia, Universidade Federal de São Carlos - UFSCar, CP 676, 13561-901, São Carlos, SP, Brazil
| | - Eduardo E Castellano
- Instituto de Física de São Carlos, Universidade de São Paulo - USP, CP 369, CEP 13560-970, São Carlos, SP, Brazil
| | - Alzir A Batista
- Departamento de Química, Universidade Federal de São Carlos - UFSCar, CP 676, CEP 13561-901, São Carlos, SP, Brazil.
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Wang Q, Heo W, Choi S, Jang W, Lim CS, Jung HI. Hand-held all-in-one (HAO) self-test kit for rapid and on-site detection of SARS-CoV-2 with colorimetric LAMP. LAB ON A CHIP 2024; 24:3265-3275. [PMID: 38847067 DOI: 10.1039/d4lc00199k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Throughout the COVID-19 pandemic, individuals potentially infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were forcibly recalled to local or central hospitals, where the diagnostic results were obtained a couple of days after the liquid biopsies were subjected to conventional polymerase chain reaction (PCR). This slow output of such a complex and time-consuming laboratory procedure hindered its widespread application. To overcome the limitations associated with such a centralized diagnostic system, we developed a hand-held and all-in-one type test kit in which the analytical results can be obtained in only 30 min. The test kit consists of three major steps for on-site SARS-CoV-2 RNA detection: 1) virus lysis by heat, 2) RNA enrichment by membrane, and 3) real-time detection by colorimetric loop-mediated isothermal amplification (c-LAMP). The proposed device operates in a sample-to-answer format, is fully automated, and reduces dependence on traditional laboratory settings, facilitating large-scale population screening.
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Affiliation(s)
- Qingyang Wang
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Woong Heo
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Seoyeon Choi
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
- The DABOM Inc., Seoul, 03722, Republic of Korea
| | - Woongsik Jang
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Hyo-Il Jung
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
- The DABOM Inc., Seoul, 03722, Republic of Korea
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Rijwan, Arjmand F, Tabassum S. Repurposing the antihistamine drug bilastine as an anti-cancer metallic drug entity: synthesis and single-crystal X-ray structure analysis of metal-based bilastine and phen [Co(II), Cu(II) and Zn(II)] tailored anticancer chemotherapeutic agents against resistant cancer cells. Dalton Trans 2024; 53:10126-10141. [PMID: 38817206 DOI: 10.1039/d4dt00426d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Bilastine (BLA), 2-(4-(2-(4-(1-(2-ethoxyethyl)-1H-benzo[d]imidazole-2-yl)-piperidin-1-yl)-ethyl)-phenyl)-2-methylpropanoic acid, is an active antihistamine drug. With the idea of repurposing drugs from the existing pool of 'active' pharmaceutical ingredients, the therapeutic potency of bilastine as an anticancer agent was investigated via the tailored synthesis of a metal-based anticancer drug formulation of the type [BLA(phen)2M(II)]+·X-, where M = Co, Cu, and Zn and X- = NO3 and ClO4. The synthesized metal-based chemotherapeutics derived from the bilastine drug that acts as a ligand were thoroughly characterized using spectroscopic techniques, namely, UV-vis, FT-IR, and EPR (in the case of 1 and 2); 1H-NMR and 13C-NMR (in the case of 3); ESI-MS and single-crystal X-ray diffraction studies. Comprehensive biological studies (DNA binding, cleavage, and cytotoxic activity) using various biophysical and gel electrophoretic methods were carried out to validate their potential as anticancer agents. The cytotoxic activity of 'therapeutically promising' copper(II)-based drug candidate 2 was evaluated against MCF-7, MBA-MD-231, HeLa, HepG2, and Mia-PaCa-2 cancer cells via an SRB assay, and the results demonstrated 2 as a potent anticancer agent at low nanomolar concentrations against all tested cancer cells, preferably with a much superior anticancer efficacy against human pancreatic cancer cells.
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Affiliation(s)
- Rijwan
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India.
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India.
| | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India.
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Brossard EE, Corcelli SA. Mechanism of Daunomycin Intercalation into DNA from Enhanced Sampling Simulations. J Phys Chem Lett 2024; 15:5770-5778. [PMID: 38776167 DOI: 10.1021/acs.jpclett.4c00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Daunomycin is a widely used anticancer drug, yet the mechanism underlying how it binds to DNA remains contested. 469 all-atom trajectories of daunomycin binding to the DNA oligonucleotide d(GCG CAC GTG CGC) were collected using weighted ensemble (WE)-enhanced sampling. Mechanistic insights were revealed through analysis of the ensemble of trajectories. Initially, the binding process involves a ubiquitous hydrogen bond between the DNA backbone and the NH3+ group on daunomycin. During the binding process, most trajectories exhibited similar structural changes to DNA, including DNA base pair rise, bending, and minor groove width changes. Variability within the ensemble of binding trajectories illuminates differences in the orientation of daunomycin as it initially intercalates; around 10% of trajectories needed minimal rearrangement from intercalation to reaching the fully bound configuration, whereas most needed an additional 1-5 ns to rearrange. The results here emphasize the utility of generating an ensemble of trajectories to discern biomolecular binding mechanisms.
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Affiliation(s)
- E E Brossard
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Tulsiyan KD, Panda SK, Rana MK, Biswal HS. Critical assessment of interactions between ct-DNA and choline-based magnetic ionic liquids: evidences of compaction. Chem Sci 2024; 15:5507-5515. [PMID: 38638223 PMCID: PMC11023040 DOI: 10.1039/d4sc00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
Ionic liquids (ILs) have become an alternative green solvent for storage and for stability of DNA. However, an in-depth understanding of binding and molecular interactions between ILs and DNA is needed. In this respect, magnetic ILs (MILs) are promising due to their tunable physicochemical properties. Various spectroscopic techniques and molecular simulations have been employed to unravel the critical factors of the strength and binding mechanism of MILs with DNA. UV-vis spectra unravel the multimodal binding of MILs with DNA, and the intrusion of IL molecules into the minor groove of DNA has been observed from dye displacement studies. Fluorescence correlation spectroscopic studies and scanning electron microscopy confirm the compaction of the DNA. ITC and molecular docking studies estimate the binding affinity of DNA with MILs, of ∼7 kcal mol-1. The 1 μs long-MD simulations give insight into the structural changes in the DNA in the MIL environment. Due to strong interaction with choline ions in the close vicinity, DNA helixes bend or squeeze in length and dilate in diameter (elliptical → spherical), leading to compaction. The post-MD parameters suggest a stronger interaction with [Ch]2[Mn] IL than with [Ch][Fe] IL; hence, the former induces DNA compaction to a more significant extent. Furthermore, decompaction is observed with the addition of sodium salts and is characterized using spectroscopic methods.
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Affiliation(s)
- Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur Odisha-760010 India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur Odisha-760010 India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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Anika, Singh S, Rimpi. Neuroprotective effects of Embelin in an ethidium bromide-induced multiple sclerosis in rats: Modulation of p38 MAPK signaling pathway. Int Immunopharmacol 2024; 129:111639. [PMID: 38335654 DOI: 10.1016/j.intimp.2024.111639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Multiple sclerosis (MS) is a debilitating inflammatory disease characterized by demyelination, varied remyelination conservation, and partial axonal retention in central nervous system (CNS) lesions. The p38 mitogen-activated protein kinase (MAPK) pathway has been implicated in the pathophysiology of MS. Embelin (EMB), derived from the Embelia ribes plant, possesses diverse biological activities, including anti-inflammatory properties. OBJECTIVE This study aimed to investigate the neuroprotective effects of EMB in an ethidium bromide (EB)-induced model of MS in Wistar rats. METHODS Wistar rats were randomly divided into five groups (n = 8). MS-like manifestations were induced by injecting EB (0.1 %/10 µl) into the intracerebropeduncle (ICP) region of the rat brain for seven consecutive days. EMB was administered at doses of 1.25, 2.5, and 5 mg/kg. Behavioral assessments, neuroinflammatory cytokine analysis like tumor necrosis factor-α, interleukin-1-β, interleukin-6 (TNF-α, IL-1β, IL-6), oxidative stress marker measurements malondialdehyde, reduced glutathione, superoxide dismutase (MDA, GSH, SOD), and nitrite (NO), Acetylcholinesterase enzyme (AchE), and neurotransmitter level analysis, dopamine, serotonin, and norepinephrine (DA, 5-HT, and NE) were conducted. RESULTS The study assessed behavioral, neurochemical, biochemical, and neuroinflammatory parameters, along with the modulation of p38 MAPK signaling. EMB administration significantly ameliorated neurological consequences induced by EB, improving motor coordination and gait abnormalities in rats. Furthermore, EMB effectively reduced neuroinflammatory cytokines (TNF-α, IL-1β, IL-6) and oxidative stress markers (AchE, SOD, MDA, GSH, nitrite). Notably, EMB exhibited a modulatory effect on neurotransmitter levels, increasing GABA, DA, and 5-HT, while reducing glutamate in EB-treated groups. CONCLUSION This study demonstrates the neuroprotective potential of EMB against the EB-induced model of MS in rats. EMB administration mitigated neurological impairments, attenuated neuroinflammation, alleviated oxidative stress, and restored neurotransmitter balance. These findings highlight the promise of EMB as a therapeutic candidate for MS treatment, providing insights into its potential mechanism of action involving the modulation of p38 MAPK signaling.
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Affiliation(s)
- Anika
- Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab 142001, India
| | - Shamsher Singh
- Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab 142001, India
| | - Rimpi
- Pharma Innovation Lab, Dept. of Pharmaceutical Sciences &Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda 151001, India.
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Kremer M, Schulze S, Eisenbruch N, Nagel F, Vogt R, Berndt L, Dörre B, Palm GJ, Hoppen J, Girbardt B, Albrecht D, Sievers S, Delcea M, Baumann U, Schnetz K, Lammers M. Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism. Nat Commun 2024; 15:1674. [PMID: 38395951 PMCID: PMC10891134 DOI: 10.1038/s41467-024-46039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.
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Affiliation(s)
- Magdalena Kremer
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Nadja Eisenbruch
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Felix Nagel
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Vogt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Leona Berndt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Babett Dörre
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Jens Hoppen
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Britta Girbardt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Michael Lammers
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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Zhang X, Zhou C, Hou J, Feng G, Xu Z, Shao Y, Yang C, Xu G. Conjugated Oligoelectrolyte with DNA Affinity for Enhanced Nuclear Imaging and Precise DNA Quantification. BIOSENSORS 2024; 14:105. [PMID: 38392025 PMCID: PMC10887168 DOI: 10.3390/bios14020105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
Precise DNA quantification and nuclear imaging are pivotal for clinical testing, pathological diagnosis, and drug development. The detection and localization of mitochondrial DNA serve as crucial indicators of cellular health. We introduce a novel conjugated oligoelectrolyte (COE) molecule, COE-S3, featuring a planar backbone composed of three benzene rings and terminal side chains. This unique amphiphilic structure endows COE-S3 with exceptional water solubility, a high quantum yield of 0.79, and a significant fluorescence Stokes shift (λex = 366 nm, λem = 476 nm), alongside a specific fluorescence response to DNA. The fluorescence intensity correlates proportionally with DNA concentration. COE-S3 interacts with double-stranded DNA (dsDNA) through an intercalation binding mode, exhibiting a binding constant (K) of 1.32 × 106 M-1. Its amphiphilic nature and strong DNA affinity facilitate its localization within mitochondria in living cells and nuclei in apoptotic cells. Remarkably, within 30 min of COE-S3 staining, cell vitality can be discerned through real-time nuclear fluorescence imaging of apoptotic cells. COE-S3's high DNA selectivity enables quantitative intracellular DNA analysis, providing insights into cell proliferation, differentiation, and growth. Our findings underscore COE-S3, with its strategically designed, shortened planar backbone, as a promising intercalative probe for DNA quantification and nuclear imaging.
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Affiliation(s)
- Xinmeng Zhang
- Shenzhen Testing Center of Medical Devices, Shenzhen Institute for Drug Control, Shenzhen 518057, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Cheng Zhou
- Institute of Polymer Optoelectronic Materials and Devices, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Jianxun Hou
- Shenzhen Testing Center of Medical Devices, Shenzhen Institute for Drug Control, Shenzhen 518057, China
| | - Gang Feng
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Zhourui Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yonghong Shao
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Chengbin Yang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Gaixia Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
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11
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Huang Z, Li P, Lei Y, Deng XY, Chen YN, Tian S, Pan X, Lei X, Song C, Zheng Y, Wang JY, Zhang Z, Lei T. Azonia-Naphthalene: A Cationic Hydrophilic Building Block for Stable N-Type Organic Mixed Ionic-Electronic Conductors. Angew Chem Int Ed Engl 2024; 63:e202313260. [PMID: 37938169 DOI: 10.1002/anie.202313260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/09/2023]
Abstract
Conjugated polymers that can efficiently transport both ionic and electronic charges have broad applications in next-generation optoelectronic, bioelectronic, and energy storage devices. To date, almost all the conjugated polymers have hydrophobic backbones, which impedes efficient ion diffusion/transport in aqueous media. Here, we design and synthesize a novel hydrophilic polymer building block, 4a-azonia-naphthalene (AN), drawing inspiration from biological systems. Because of the strong electron-withdrawing ability of AN, the AN-based polymers show typical n-type charge transport behaviors. We find that cationic aromatics exhibit strong cation-π interactions, leading to smaller π-π stacking distance, interesting ion diffusion behavior, and good morphology stability. Additionally, AN enhances the hydrophilicity and ionic-electronic coupling of the polymer, which can help to improve ion diffusion/injection speed, and operational stability of organic electrochemical transistors (OECTs). The integration of cationic building blocks will undoubtedly enrich the material library for high-performance n-type conjugated polymers.
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Affiliation(s)
- Zhen Huang
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peiyun Li
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Yuqiu Lei
- College of Engineering, Peking University, Beijing, 100871, China
| | - Xin-Yu Deng
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Yu-Nan Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Shuangyan Tian
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Xiran Pan
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Xun Lei
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Cheng Song
- College of Engineering, Peking University, Beijing, 100871, China
| | - Yuting Zheng
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Jie-Yu Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhi Zhang
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Ting Lei
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, School of Materials Science and Engineering, Peking University, Beijing, 100871, China
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12
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Love O, Winkler L, Cheatham TE. van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD. J Chem Theory Comput 2024; 20:625-643. [PMID: 38157247 PMCID: PMC10809421 DOI: 10.1021/acs.jctc.3c01164] [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: 10/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
Molecular dynamics simulations can be used in combination with experimental techniques to uncover the intricacies of biomolecular structure, dynamics, and the resulting interactions. However, many noncanonical nucleic acid structures have proven to be challenging to replicate in accurate agreement with experimental data, often attributed to known force field deficiencies. A common force field criticism is the handling of van der Waals (vdW) parameters, which have not been updated since the regular use of Ewald's methods became routine. This work dives into the effects of minute vdW radii shifts on RNA tetranucleotide, B-DNA, and Z-DNA model systems described by commonly used Amber force fields. Using multidimensional replica exchange molecular dynamics (M-REMD), the GACC RNA tetranucleotide demonstrated changes in the structural distribution between the NMR minor and anomalous structure populations based on the O2' vdW radii scanning. However, no significant change in the NMR Major conformation population was observed. There were minimal changes in the B-DNA structure but there were more substantial improvements in Z-DNA structural descriptions, specifically with the Tumuc1 force field. This occurred with both LJbb vdW radii adjustments and incorporation of the CUFIX nonbonded parameter modifications. Though the limited vdW modifications tested did not provide a universal fix to the challenge of simulating the various known nucleic acid structures, they do provide direction and a greater understanding for future force field development efforts.
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Affiliation(s)
| | | | - Thomas E. Cheatham
- Department of Medicinal Chemistry,
College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112, United States
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13
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Ypsilantis K, Sifnaiou E, Garypidou A, Kordias D, Magklara A, Garoufis A. Ruthenium-Cyclopentadienyl-Cycloparaphenylene Complexes: Sizable Multicharged Cations Exhibiting High DNA-Binding Affinity and Remarkable Cytotoxicity. Molecules 2024; 29:514. [PMID: 38276592 PMCID: PMC10818589 DOI: 10.3390/molecules29020514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Two novel sizable multicharged cationic complexes, of the formulae [(η6--[12]CPP)[Ru(η5--Cp)]12]Χ12 and [(η6--[11]CPP)[Ru(η5--Cp)]11]Χ11, CPP = cycloparaphenylene, Cp = cyclopentadienyl, X = [PF6]-, (1), (3) and [Cl]-, (2), (4), were synthesized and characterized using NMR techniques, high-resolution mass spectrometry, and elemental analyses. Complexes (1) and (3) were stable in acetone and acetonitrile solutions over 48 h. In contrast, the water-soluble (2) and (4) begin to decompose in aqueous media after 1 h, due to the [Cl]- tendency for nucleophilic attack on ruthenium of the {Ru(η5--Cp)} units. Fluorescence quenching experiments conducted during the stability window of (2) with the d(5'-CGCGAATTCGCG-3')2-EtBr adducts revealed remarkably high values for Ksv = 1.185 × 104 ± 0.025 M-1 and Kb = 3.162 × 105 ± 0.001 M-1. Furthermore, the cytotoxic activity of (2) against A2780, A2780res, and MCF-7 cancer cell lines shows that it is highly cytotoxic with IC50 values in the range of 4.76 ± 1.85 to 16 ± 0.81 μΜ.
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Affiliation(s)
- Konstantinos Ypsilantis
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (K.Y.); (E.S.); (A.G.)
| | - Evangelia Sifnaiou
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (K.Y.); (E.S.); (A.G.)
| | - Antonia Garypidou
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (K.Y.); (E.S.); (A.G.)
| | - Dimitrios Kordias
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece; (D.K.); (A.M.)
- Laboratory of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Angeliki Magklara
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece; (D.K.); (A.M.)
- Laboratory of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
- Institute of Biosciences, University Research Center of Ioannina (U.R.C.I.), 45110 Ioannina, Greece
| | - Achilleas Garoufis
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (K.Y.); (E.S.); (A.G.)
- Institute of Materials Science and Computing, University Research Centre of Ioannina (U.R.C.I.), 45110 Ioannina, Greece
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14
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Sifnaiou E, Tsolis T, Ypsilantis K, Roupakia E, Kolettas E, Plakatouras JC, Garoufis A. Synthesis and Characterization of Ruthenium-Paraphenylene-Cyclopentadienyl Full-Sandwich Complexes: Cytotoxic Activity against A549 Lung Cancer Cell Line and DNA Binding Properties. Molecules 2023; 29:17. [PMID: 38202599 PMCID: PMC10780011 DOI: 10.3390/molecules29010017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Novel full-sandwich (η5-Cp)-Ru-paraphenylene complexes with the general formula [(η5-Cp)nRu(η6-L)](PF6)n where n = 1-3 and L = biphenyl, p-terphenyl and p-quaterphenyl, were synthesized and characterized by means of spectroscopic and analytical techniques. The structures of the complexes [(η5-Cp)Ru(η6-biphenyl)](PF6) (1), [(η5-Cp)Ru(η6-terphenyl)](PF6) (3) and [(η5-Cp)2Ru(η6-terphenyl)](PF6)2 (4) was determined by X-ray single crystal methods. The interaction of the complexes [(η5-Cp)Ru(η6-quaterphenyl)]Cl, (6)Cl, and [(η5-Cp)2Ru(η6-quaterphenyl)]Cl2, (7)Cl2, with the DNA duplex d(5'-CGCGAATTCGCG-3')2 was studied using NMR techniques. The results showed that both complexes interacted non-specifically with both the minor and major grooves of the helix. Specifically, (6)Cl exhibited partial binding through intercalation between the T7 and T8 bases of the sequence without disrupting the C-G and A-T hydrogen bonds. Fluorometric determination of the complexes' binding constants revealed a significant influence of the number of connected phenyl rings in the paraphenylene ligand (L) on the binding affinity of their complexes with the d(5'-CGCGAATTCGCG-3')2. The complexes (6)Cl and (7)Cl2 were found to be highly cytotoxic against the A549 lung cancer cell line, with complex (6) being more effective than (7) (IC50 for (6)Cl: 17.45 ± 2.1 μΜ, IC50 for (7)Cl2: 65.83 ± 1.8 μΜ) and with a selectivity index (SI) (SI for (6)Cl: 1.1 and SI for (7)Cl2: 4.8).
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Affiliation(s)
- Evangelia Sifnaiou
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.S.); (T.T.); (K.Y.); (J.C.P.)
| | - Theodoros Tsolis
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.S.); (T.T.); (K.Y.); (J.C.P.)
| | - Konstantinos Ypsilantis
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.S.); (T.T.); (K.Y.); (J.C.P.)
| | - Eugenia Roupakia
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.R.); (E.K.)
- Institute of Biomedical Research, Foundation for Research and Technology, 45110 Ioannina, Greece
| | - Evangelos Kolettas
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (E.R.); (E.K.)
- Institute of Biomedical Research, Foundation for Research and Technology, 45110 Ioannina, Greece
| | - John C. Plakatouras
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.S.); (T.T.); (K.Y.); (J.C.P.)
- Institute of Materials Science and Computing, University Research Centre of Ioannina (URCI), 45110 Ioannina, Greece
| | - Achilleas Garoufis
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.S.); (T.T.); (K.Y.); (J.C.P.)
- Institute of Materials Science and Computing, University Research Centre of Ioannina (URCI), 45110 Ioannina, Greece
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15
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Wu HY, Cao Z, Li SQ, Fu YW, Li JM, Li XH, He CM, Chen JY. Visible-Light-Mediated Annulation/Thiolation of 2-Isocyanobiaryls with Disulfides to Organoylthiophenanthridines Derivatives. J Org Chem 2023. [PMID: 38044560 DOI: 10.1021/acs.joc.3c02152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
A visible-light-induced annulation/thiolation of 2-isocyanobiaryls with dialkyl(aryl)disulfides has been established, delivering a sustainable and atom-economic route to 6-organoylthiophenanthridines with wild functional group tolerance and good to excellent yields under oxidant-, base-, and transition-metal-free conditions.
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Affiliation(s)
- Hong-Yu Wu
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Zhong Cao
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Changsha University of Science and Technology, Changsha, Hunan 410114, China
| | - Shi-Qi Li
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing 408000, China
| | - Yu-Wei Fu
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing 408000, China
| | - Jia-Min Li
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing 408000, China
| | - Xing-Hong Li
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing 408000, China
| | - Chun-Mei He
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing 408000, China
| | - Jin-Yang Chen
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing 408000, China
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16
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Koirala D, Dalbec F, May J, Hamal K, Allen PB, Cheng IF. Biosensing with Polymerase Chain Reaction-Stable DNA-Functionalized Magnetically Susceptible Carbon-Iron Microparticles. Anal Chem 2023; 95:16631-16638. [PMID: 37904495 DOI: 10.1021/acs.analchem.3c02978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
We demonstrate a rapid and sensitive method for DNA detection without the need for fluorescence. This is based on carbon-coated magnetic iron (Fe) microparticles with a covalent surface attachment of DNA. We show that these magnetic microparticles can capture complementary DNA. Significantly, the DNA covalent surface bonds are robust to high temperatures and can be included in a sample during polymerase chain reaction (PCR). This method is employed for the detection of targeted DNA sequences (40-50 bp). Hybridization probes on the surface of the magnetically susceptible Fe microparticle recognize the target DNA sequence-specifically. The double-stranded DNA (dsDNA) microparticles are then quickly captured with a magnet from the sample matrix. This foregoes postpurification processes, such as electrophoresis, which make our technique time- and cost-effective. Captured dsDNA can be detected with intercalating dyes such as ethidium bromide through a loss in the UV absorption signal with a limit of detection (LOD) of 24 nM within 15 min. Likewise, surface-bound DNA can act as a primer in PCR to decrease the LOD to 5 pM within 2 h. This is the first instance of a nucleotide-modified magnetically susceptible carbon substrate that is PCR-compatible. Besides DNA capture, this strategy can eventually be applied to sequence-specific nucleic acid purification and enrichment, PCR cleanup, and single-strand generation. The DNA-coated particles are stable under PCR conditions (unlike commonly used polystyrene or gold particles).
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Affiliation(s)
- Dipak Koirala
- Department of Chemistry, University of Idaho, 875 Perimeter Dr, MS 2343, Moscow, Idaho 83844, United States
| | - Forrest Dalbec
- Department of Chemistry, University of Idaho, 875 Perimeter Dr, MS 2343, Moscow, Idaho 83844, United States
| | - Jeremy May
- Department of Chemistry, University of Idaho, 875 Perimeter Dr, MS 2343, Moscow, Idaho 83844, United States
| | - Kailash Hamal
- Department of Chemistry, University of Idaho, 875 Perimeter Dr, MS 2343, Moscow, Idaho 83844, United States
| | - Peter B Allen
- Department of Chemistry, University of Idaho, 875 Perimeter Dr, MS 2343, Moscow, Idaho 83844, United States
| | - I Francis Cheng
- Department of Chemistry, University of Idaho, 875 Perimeter Dr, MS 2343, Moscow, Idaho 83844, United States
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17
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Rodrigues Dos Santos Barbosa C, Macêdo NS, de Sousa Silveira Z, Rocha JE, Freitas TS, Muniz DF, Araújo IM, Datiane de Morais Oliveira-Tintino C, Marinho ES, Nunes da Rocha M, Marinho MM, Bezerra AH, Ribeiro de Sousa G, Barbosa-Filho JM, de Souza-Ferrari J, Melo Coutinho HD, Silva Dos Santos H, Bezerra da Cunha FA. Evaluation of the antibacterial and inhibitory activity of the MepA efflux pump of Staphylococcus aureus by riparins I, II, III, and IV. Arch Biochem Biophys 2023; 748:109782. [PMID: 37839789 DOI: 10.1016/j.abb.2023.109782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
The efflux pump mechanism contributes to the antibiotic resistance of widely distributed strains of Staphylococcus aureus. Therefore, in the present work, the ability of the riparins N-(4-methoxyphenethyl)benzamide (I), 2-hydroxy-N-[2-(4-methoxyphenyl)ethyl]benzamide (II), 2, 6-dihydroxy-N-[ 2-(4-methoxyphenyl)ethyl]benzamide (III), and 3,4,5-trimethoxy-N-[2-(4-methoxyphenethyl)benzamide (IV) as potential inhibitors of the MepA efflux pump in S. aureus K2068 (fluoroquinolone-resistant). In addition, we performed checkerboard assays to obtain more information about the activity of riparins as potential inhibitors of MepA efflux and also analyzed the ability of riparins to act on the permeability of the bacterial membrane of S. aureus by the fluorescence method with SYTOX Green. A molecular coupling assay was performed to characterize the interaction between riparins and MepA, and ADMET (absorption, distribution, metabolism, and excretion) properties were analyzed. We observed that I-IV riparins did not show direct antibacterial activity against S. aureus. However, combination assays with substrates of MepA, ciprofloxacin, and ethidium bromide (EtBr) revealed a potentiation of the efficacy of these substrates by reducing the minimum inhibitory concentration (MIC). Furthermore, increased EtBr fluorescence emission was observed for all riparins. The checkerboard assay showed synergism between riparins I, II, and III, ciprofloxacin, and EtBr. Furthermore, riparins III and IV exhibited permeability in the S. aureus membrane at a concentration of 200 μg/mL. Molecular docking showed that riparins I, II, and III bound in a different region from the binding site of chlorpromazine (standard pump inhibitor), indicating a possible synergistic effect with the reference inhibitor. In contrast, riparin IV binds in the same region as the chlorpromazine binding site. From the in silico ADMET prediction based on MPO, it could be concluded that the molecules of riparin I-IV present their physicochemical properties within the ideal pharmacological spectrum allowing their preparation as an oral drug. Furthermore, the prediction of cytotoxicity in liver cell lines showed a low cytotoxic effect for riparins I-IV.
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Affiliation(s)
| | - Nair Silva Macêdo
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Zildene de Sousa Silveira
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Janaína Esmeraldo Rocha
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Thiago Sampaio Freitas
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Débora Feitosa Muniz
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | - Isaac Moura Araújo
- Biological Chemistry, Department of Biological Chemistry, Cariri Regional University (URCA), Crato, CE, Brazil.
| | | | - Emmanuel Silva Marinho
- State University of Ceará, Graduate Program in Natural Sciences, Laboratory of Natural Products Chemistry, Fortaleza, Ceará, Brazil.
| | - Matheus Nunes da Rocha
- State University of Ceará, Graduate Program in Natural Sciences, Laboratory of Natural Products Chemistry, Fortaleza, Ceará, Brazil.
| | - Marcia Machado Marinho
- Center of Exact Sciences and Technology, State University of Ceará, Fortaleza, CE, Brazil.
| | | | - Gabriela Ribeiro de Sousa
- Natural and Synthetic Bioactive Products, Federal University of Paraiba (UFPB), João Pessoa, PB, Brazil.
| | - José Maria Barbosa-Filho
- Natural and Synthetic Bioactive Products, Federal University of Paraiba (UFPB), João Pessoa, PB, Brazil.
| | | | | | - Hélcio Silva Dos Santos
- Rede Nordeste de Biotecnologia (RENORBIO-Nucleadora UECE), Universidade Estadual Vale do Acaraú (UVA), Sobral, CE, Brazil.
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18
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Lanquist AP, Piechota EJ, Wickramasinghe LD, Marques Silva A, Thummel RP, Turro C. New Tridentate Ligand Affords a Long-Lived 3MLCT Excited State in a Ru(II) Complex: DNA Photocleavage and 1O 2 Production. Inorg Chem 2023; 62:15927-15935. [PMID: 37733276 DOI: 10.1021/acs.inorgchem.3c01990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Two new complexes, [Ru(tpy)(qdppz)](PF6)2 (1; qdppz = 2-(quinolin-8-yl)dipyrido[3,2-a:2',3'-c]phenazine, tpy = 2,2':6',2″-terpyridine) and [Ru(qdppz)2](PF6)2 (2), were investigated for their potential use as phototherapeutic agents through their ability to photosensitize the production of singlet oxygen, 1O2, upon irradiation with visible light. The complexes exhibit strong Ru(dπ) → qdppz(π*) metal-to-ligand charge transfer (MLCT) absorption with maxima at 485 and 495 nm for 1 and 2 in acetone, respectively, red-shifted from the Ru(dπ) → tpy(π*) absorption at 470 nm observed for [Ru(tpy)2]2+ (3) in the same solvent. Complexes 1 and 3 are not luminescent at room temperature, but 3MLCT emission is observed for 2 with maximum at 690 nm (λexc = 480 nm) in acetone. The lifetimes of the 3MLCT states of 1 and 2 were measured using transient absorption spectroscopy to be ∼9 and 310 ns in methanol, respectively, at room temperature (λexc = 490 nm). The bite angle of the qdppz ligand is closer to octahedral geometry than that of tpy, resulting in the longer lifetime of 2 as compared to those of 1 and 3. Arrhenius treatment of the temperature dependence of the luminescence results in similar activation energies, Ea, from the 3MLCT to the 3LF (ligand-field) state for the two complexes, 2520 cm-1 in 1 and 2400 cm-1 in 2. However, the pre-exponential factors differ by approximately two orders of magnitude, 2.3 × 1013 s-1 for 1 and 1.4 × 1011 s-1 for 2, which, together with differences in the Huang-Rhys factors, lead to markedly different 3MLCT lifetimes. Although both 1 and 2 intercalate between the DNA bases, only 2 is able to photocleave DNA owing to its 1O2 production upon irradiation with ΦΔ = 0.69. The present work highlights the profound effect of the ligand bite angle on the electronic structure, providing guidelines for extending the lifetime of 3MLCT Ru(II) complexes with tridentate ligands, a desired property for a number of applications.
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Affiliation(s)
- Austin P Lanquist
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eric J Piechota
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Alexia Marques Silva
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Randolph P Thummel
- Department of Chemistry, University of Houston, Houston, Texas 77004, United States
| | - Claudia Turro
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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19
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Ju P, Zhu YY, Jiang TT, Gao G, Wang SL, Jiang XW, Xu YT, Zhai XF, Zhou H, Zhao WW. DNA intercalation makes possible superior-gain organic photoelectrochemical transistor detection. Biosens Bioelectron 2023; 237:115543. [PMID: 37499378 DOI: 10.1016/j.bios.2023.115543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
DNA intercalation has increasingly been studied for various scenario implementations due to the diverse functions of DNA/intercalators. Nascent organic photoelectrochemical transistor (OPECT) biosensing taking place in organic electronics and photoelectrochemical bioanalysis represents a promising technological frontier in the arena. In this work, we first devise DNA intercalation-enabled OPECT for miRNA detection with a superior gain up to 17100. Intercalation of [Ru(bpy)2dppz]2+ within the miRNA-initiated hybrid chain reaction (HCR)-derived duplex DNA is realized for producing anodic photocurrent upon light stimulation, causing the corresponding target-dependent alternation in gate voltage (VG) and hence the modulated channel current (IDS) of poly (3,4-ethylenedioxythiophene) doped with poly (styrene sulfonate) (PEDOT:PSS) under specific drain voltage (VDS) for quantitative miRNA-21 analysis, which shows a wide linear relationship and a low detection limit of 5.5 × 10-15 mol L-1. This study features the DNA intercalation-enabled organic electronics with superior gain and is envisaged to attract more attention to explore DNA adducts for innovative bioelectronics and biosensing, given the diverse DNA binders with multiple functions.
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Affiliation(s)
- Peng Ju
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; Shandong Key Laboratory of Marine Ecological Environment and Disaster Prevention and Mitigation, Qingdao, 266061, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China
| | - Yu-Yue Zhu
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; College of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Tian-Tong Jiang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China
| | - Ge Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Shi-Liang Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China
| | - Xing-Wu Jiang
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao, 266061, China; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China; Shandong Key Laboratory of Marine Ecological Environment and Disaster Prevention and Mitigation, Qingdao, 266061, China
| | - Yi-Tong Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xiao-Fan Zhai
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao, 266071, China.
| | - Hong Zhou
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
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20
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Brossard EE, Corcelli SA. Molecular Mechanism of Ligand Binding to the Minor Groove of DNA. J Phys Chem Lett 2023; 14:4583-4590. [PMID: 37163748 DOI: 10.1021/acs.jpclett.3c00635] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Although DNA-ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling, an ensemble of 2562 binding trajectories of Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the binding mechanism was extracted. In particular, the electrostatic interaction between the positively charged H33258 and the negatively charged DNA backbone drives the formation of initial H33258-DNA contacts. After this initial contact, a hinge-like intermediate state is formed in which one end of H33258 inserts into the minor groove of DNA. Following hinge state formation is a concerted motion whereby the second end of H33258 swings into the minor groove and the spine of hydration along the minor groove causing dehydration. This study illustrates how WE-enhanced simulations of biomolecular ligation processes can offer novel mechanistic insights by generating ensembles of binding events.
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Affiliation(s)
- E E Brossard
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - S A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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21
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Pronkin PG, Tatikolov AS. Spectral-fluorescent and photochemical study of 6,6'-di(benzoylamino)trimethine cyanine dyes in solutions as possible probes for DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122416. [PMID: 36746042 DOI: 10.1016/j.saa.2023.122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Spectral-fluorescent and photochemical properties of trimethine cyanine dyes T-304, T-306, and T-307, having substituents in 6,6'-positions, in various organic solvents, in aqueous buffer solutions, in the presence of surfactants and ethanol additives, and the effect on these properties of addition of DNA have been studied. Strong aggregation of the dyes in aqueous and aqueous buffer solutions has been shown. This is due to increased hydrophobicity of the dyes, which makes it difficult to use them as spectral-fluorescent probes for DNA. In the presence of DNA, trimethine cyanines partially form highly fluorescent complexes of dye monomers with the biomolecule, with slight decomposition of the initial aggregates and the formation of aggregates on DNA molecules. The formation of different types of dye-DNA complexes, i.e., intercalation and binding in the DNA grooves, was modeled by molecular docking. Dye-DNA complexes were also studied by circular dichroism spectroscopy and by thermal dissociation of DNA. To reveal selectivity of the dyes, their interaction with human serum albumin was briefly studied. The presence of moderate concentrations of nonionic surfactants does not lead to a significant decomposition of aggregates, but leads to a biphasic dependence of the fluorescence intensity on the DNA concentration. At the same time, ethanol additives (15%) lead to a more or less linear concentration dependence of the fluorescence intensity, which makes it possible to use these dyes as fluorescent probes for DNA. The effective binding constants of the dyes to DNA and the limits of DNA detection using the dyes in the presence of 15% ethanol were estimated. Photoisomerization and generation of the triplet states of T-304, T-306, and T-307 have been also studied. Along with the fluorescence growth, complexation with DNA leads to an increase in the yield of the triplet states of the dyes. This creates a prerequisite for using the dyes in targeted PDT. In the presence of DNA, the decay kinetics of the triplet states are biexponential, which indicates different types of dye complexes with DNA. The rate constants of oxygen quenching of the triplet states of the dyes bound to DNA are significantly lower than the diffusion-controlled values (taking into account the spin-statistical factor), which is explained by the shielding effect on the triplet molecules in complexes with DNA. The data obtained show that dyes T-304, T-306 and T-307, with addition of 15% ethanol, can be used as possible fluorescent probes for DNA.
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Affiliation(s)
- P G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia.
| | - A S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Str., 119334 Moscow, Russia
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22
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Baral B, Nial PS, Subudhi U. Enhanced enzymatic activity and conformational stability of catalase in presence of tetrahedral DNA nanostructures: A biophysical and kinetic study. Int J Biol Macromol 2023; 242:124677. [PMID: 37141969 DOI: 10.1016/j.ijbiomac.2023.124677] [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: 02/26/2023] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
The emergence of DNA nanotechnology has shown enormous potential in a vast array of applications, particularly in the medicinal and theranostics fields. Nevertheless, the knowledge of the compatibility between DNA nanostructures and cellular proteins is largely unknown. Herein, we report the biophysical interaction between proteins (circulatory protein bovine serum albumin, BSA, and the cellular enzyme bovine liver catalase, BLC) and tetrahedral DNA (tDNAs), which are well-known nanocarriers for therapeutics. Interestingly, the secondary conformation of BSA or BLC was unaltered in the presence of tDNAs which supports the biocompatible property of tDNA. In addition, thermodynamic studies showed that the binding of tDNAs with BLC has a stable non-covalent interaction via hydrogen bond and van der Waals contact, which is indicative of a spontaneous reaction. Furthermore, the catalytic activity of BLC was increased in the presence of tDNAs during 24 h of incubation. These findings indicate that the presence of tDNA nanostructures not only ensures a steady secondary conformation of proteins, but also stabilize the intracellular proteins like BLC. Surprisingly, our investigation discovered that tDNAs have no effect on albumin proteins, either by interfering or by adhering to the extracellular proteins. These findings will aid in the design of future DNA nanostructures for biomedical applications by increasing the knowledge on the biocompatible interaction of tDNAs with biomacromolecules.
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Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; School of Biological Sciences, Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Partha S Nial
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; School of Biological Sciences, Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; School of Biological Sciences, Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
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23
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Maity D, Bhaumik SK, Banerjee S. Contrasting luminescence in heparin and DNA-templated co-assemblies of dimeric cyanostilbenes: efficient energy transfer in heparin-based co-assemblies. Phys Chem Chem Phys 2023; 25:12810-12819. [PMID: 37129214 DOI: 10.1039/d3cp00709j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dimeric cationic cyanostilbenes with peripheral alkyl chains demonstrated aggregation in aqueous media depending on the length of the hydrophobic segment and produced luminescent spherical nano-assemblies in the case of long alkyl chain derivatives. In the presence of heparin, a bio-polyanion that is routinely used as an anticoagulant, the self-assembled structures obtained from the amphiphilic dimers showed the formation of higher-order structures whereas the non-assembling dimers exhibited heparin-induced supramolecular structure formation. In both cases, a significant enhancement in the emission was observed. This led to the detection of heparin in aqueous buffer, serum and plasma with a "turn-on" fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA. However, the response towards DNA was opposite to that observed in the case of heparin i.e., "turn-off'' fluorescence response. Notably, depending on the length of the alkyl segment, divergent DNA binding modes of these derivatives were observed. Due to their enhanced luminescence, the heparin-based co-assemblies were further explored as artificial light-harvesting systems exhibiting an efficient energy transfer process to embedded acceptor dyes with a high antenna effect.
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Affiliation(s)
- Dhananjoy Maity
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Shubhra Kanti Bhaumik
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
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24
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Wang Y, Shi N, He Y, Li Y, Zheng Q. A direct approach toward investigating DNA-ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:2153-2160. [PMID: 36562542 DOI: 10.1039/d2cp04566d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small molecules that interfere with DNA replication can trigger genomic instability, which makes these molecules valuable in the search for anticancer drugs. Thus, interactions between DNA and its ligands at the molecular level are of great significance. In the present study, a new method based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations has been proposed for analyzing the interactions between DNA and its ligands. The SERS signals of DNA hairpins (ST: d(CGACCAACGTGTCGCCTGGTCG), AP1: d(CGCACAACGTGTCGCCTGTGCG)), pure argininamide, and their complexes, were obtained, and the characteristic peak sites of the DNA secondary structure and argininamide ligand-binding region were analyzed. Molecular dynamics calculations predicted that argininamide binds to the 8C and 9G bases of AP1 via hydrogen bonding. Our method successfully detected the changes of SERS fingerprint peaks of hydrogen bonds and bases between argininamide and DNA hairpin bases, and their binding sites and action modes were consistent with the predicted results of the molecular dynamics simulations. This SERS technology combined with the molecular dynamics simulation detection platform provides a general analysis tool, with the advantage of effective, rapid, and sensitive detection. This platform can obtain sufficient molecular level conformational information to provide avenues for rapid drug screening and promote progress in several fields, including targeted drug design.
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Affiliation(s)
- Yunpeng Wang
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Na Shi
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
| | - Yingying He
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Yang Li
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
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25
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Bera M, Das M, Dolai M, Laha S, Islam MM, Samanta BC, Das A, Choudhuri I, Bhattacharyya N, Maity T. DNA/Protein Binding and Apoptotic-Induced Anticancer Property of a First Time Reported Quercetin-Iron(III) Complex Having a Secondary Anionic Residue: A Combined Experimental and Theoretical Approach. ACS OMEGA 2023; 8:636-647. [PMID: 36643564 PMCID: PMC9835804 DOI: 10.1021/acsomega.2c05790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
A new quercetin-based iron(III) cationic complex [Fe(Qr)Cl(H2O)(MeO)] (complex 1) is created in the current study by condensation of quercetin with ferric chloride in the presence of Et3N. Comprehensive spectroscopic analysis and conductometric measurement are used to pinpoint complex 1. The generated complex's +3-oxidation state has been verified by electron paramagnetic resonance (EPR) research. Density functional theory analysis was used to structurally optimize the structure of complex 1. Before biomedical use, a variety of biophysical studies are implemented to evaluate the binding capacity of complex 1 with DNA and human serum albumin (HSA) protein. The findings of the electronic titration between complex 1 and DNA, as well as the stunning fall in the fluorescence intensities of the HSA and EtBr-DNA/DAPI-DNA domain after complex 1 is gradually added, give us confidence that complex 1 has a strong affinity for both macromolecules. It is interesting to note that the displacement experiment confirms partial intercalation as well as the groove binding mechanism of the title complex with DNA. The time-dependent fluorescence analysis indicates that after interaction with complex 1, HSA will exhibit static quenching. The thermodynamic parameter values in the HSA-complex 1 interaction provide evidence for the hydrophobicity-induced pathway leading to spontaneous protein-complex 1 interaction. The two macromolecules' configurations are verified to be preserved when they are associated with complex 1, and this is done via circular dichroism spectral titration. The molecular docking investigation, which is a theoretical experiment, provides complete support for the experimental findings. The potential of the investigated complex to be an anticancer drug has been examined by employing the MTT assay technique, which is carried out on HeLa cancer cell lines and HEK-293 normal cell lines. The MTT assay results validate the ability of complex 1 to display significant anticancer properties. Finally, by using the AO/PI staining approach, the apoptotic-induced cell-killing mechanism as well as the detection of cell morphological changes has been confirmed.
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Affiliation(s)
- Manjushree Bera
- Department
of Nutrition, Prabhat Kumar College, Contai, Purba Medinipur, Contai721404, India
| | - Manik Das
- Department
of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur, Contai721404, India
| | - Malay Dolai
- Department
of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur, Contai721404, India
| | - Soumik Laha
- IICB,
Kolkata, Kolkata, 700032West Bengal, India
| | - Md Maidul Islam
- Department
of Chemistry, Aliah University, Kolkata700064, India
| | - Bidhan Chandra Samanta
- Department
of Chemistry, Mugberia Gangadhar Mahavidyalaya, Purba Medinipur, Contai721425, India
| | - Arindam Das
- Department
of Chemistry, Jadavpur University, Kolkata700032, India
| | | | | | - Tithi Maity
- Department
of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur, Contai721404, India
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26
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Goel H, Goyal K, Pandey AK, Benjamin M, Khan F, Pandey P, Mittan S, Iqbal D, Alsaweed M, Alturaiki W, Madkhali Y, Kamal MA, Tanwar P, Upadhyay TK. Elucidations of Molecular Mechanism and Mechanistic Effects of Environmental Toxicants in Neurological Disorders. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2023; 22:84-97. [PMID: 35352654 DOI: 10.2174/1871527321666220329103610] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 02/08/2023]
Abstract
Due to rising environmental and global public health concerns associated with environmental contamination, human populations are continually being exposed to environmental toxicants, including physical chemical mutagens widespread in our environment causing adverse consequences and inducing a variety of neurological disorders in humans. Physical mutagens comprise ionizing and non-ionizing radiation, such as UV rays, IR rays, X-rays, which produces a broad spectrum of neuronal destruction, including neuroinflammation, genetic instability, enhanced oxidative stress driving mitochondrial damage in the human neuronal antecedent cells, cognitive impairment due to alterations in neuronal function, especially in synaptic plasticity, neurogenesis repression, modifications in mature neuronal networks drives to enhanced neurodegenerative risk. Chemical Mutagens including alkylating agents (EMS, NM, MMS, and NTG), Hydroxylamine, nitrous acid, sodium azide, halouracils are the major toxic mutagen in our environment and have been associated with neurological disorders. These chemical mutagens create dimers of pyrimidine that cause DNA damage that leads to ROS generation producing mutations, chromosomal abnormalities, genotoxicity which leads to increased neurodegenerative risk. The toxicity of four heavy metal including Cd, As, Pb, Hg is mostly responsible for complicated neurological disorders in humans. Cadmium exposure can enhance the permeability of the BBB and penetrate the brain, driving brain intracellular accumulation, cellular dysfunction, and cerebral edema. Arsenic exerts its toxic effect by induction of ROS production in neuronal cells. In this review, we summarize the molecular mechanism and mechanistic effects of mutagens in the environment and their role in multiple neurological disorders.
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Affiliation(s)
- Harsh Goel
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Keshav Goyal
- Division of Molecular and Cellular Biology, Faculty of Biology, Ludwig Maximilians Universitat, Munchen, Germany
| | - Avanish Kumar Pandey
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Mercilena Benjamin
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Fahad Khan
- Department of Biotechnology, Noida Institute of Engineering & Technology, 19, Knowledge Park-II, Institutional Area, Greater Noida, India
| | - Pratibha Pandey
- Department of Biotechnology, Noida Institute of Engineering & Technology, 19, Knowledge Park-II, Institutional Area, Greater Noida, India
| | - Sandeep Mittan
- Department of Cardiology, Ichan School of Medicine, Mount Sinai Hospital, One Gustave L. Levy Place, New York, USA
| | - Danish Iqbal
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah, 11952, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah, 11952, Saudi Arabia
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah, 11952, Saudi Arabia
| | - Yahya Madkhali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al-Majmaah, 11952, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, China
- King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Bangladesh
- Enzymoics, 7 Peterlee Place, Hebersham NSW 2770, Novel Global Community Educational Foundation, Australia
| | - Pranay Tanwar
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Cell Culture and Immunobiochemistry Lab, Centre of Research for Development, Parul University, Vadodara, Gujarat 391760, India
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27
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Amin SM, Islam T, Price NE, Wallace A, Guo X, Gomina A, Heidari M, Johnson KM, Lewis CD, Yang Z, Gates KS. Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA. ACS OMEGA 2022; 7:36888-36901. [PMID: 36278095 PMCID: PMC9583646 DOI: 10.1021/acsomega.2c05736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The experiments described here examined the effects of reaction conditions, various additives, and local sequence on the formation and stability interstrand cross-links (ICLs) derived from the reaction of an apurinic/apyrimidinic (AP) site with the exocyclic amino group of an adenine residue on the opposing strand in duplex DNA. Cross-link formation was observed in a range of different buffers, with faster formation rates observed at pH 5. Inclusion of the base excision repair enzyme alkyladenine DNA glycosylase (hAAG) which binds tightly to AP-containing duplexes decreased, but did not completely prevent, formation of the dA-AP ICL. Formation of the dA-AP ICL was not altered by the presence of the biological metal ion Mg2+ or the biological thiol, glutathione. Several organocatalysts of imine formation did not enhance the rate of dA-AP ICL formation. Duplex length did not have a large effect on dA-AP yield, so long as the melting temperature of the duplex was not significantly below the reaction temperature (the duplex must remain hybridized for efficient ICL formation). Formation of the dA-AP ICL was examined in over 40 different sequences that varied the neighboring and opposing bases at the cross-linking site. The results indicate that ICL formation can occur in a wide variety of sequence contexts under physiological conditions. Formation of the dA-AP ICL was strongly inhibited by the aldehyde-trapping agents methoxyamine and hydralazine, by NaBH3CN, by the intercalator ethidium bromide, and by the minor groove-binding agent netropsin. ICL formation was inhibited to some extent in bicarbonate and Tris buffers. The dA-AP ICL showed substantial inherent stability under a variety of conditions and was not a substrate for AP-processing enzymes APE1 or Endo IV. Finally, we characterized cross-link formation in a small (11 bp) stem-loop (hairpin) structure and in DNA-RNA hybrid duplexes.
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Affiliation(s)
- Saosan
Binth Md. Amin
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Tanhaul Islam
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Amanda Wallace
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Xu Guo
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Anuoluwapo Gomina
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Marjan Heidari
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Calvin D. Lewis
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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28
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Çeşme M, Özaltay A. DNA‐Binding Studies of Ofloxacin Using a Series of Spectroscopic, Electrochemical Techniques and in Silico Approaches. ChemistrySelect 2022. [DOI: 10.1002/slct.202202278] [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)
- Mustafa Çeşme
- Department of Chemistry Faculty of Sciences Kahramanmaras Sütçü İmam University 46040 Kahramanmaras TURKEY
| | - Ayşe Özaltay
- Department of Chemistry Faculty of Sciences Kahramanmaras Sütçü İmam University 46040 Kahramanmaras TURKEY
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29
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Ramotowska S, Spisz P, Brzeski J, Ciesielska A, Makowski M. Application of the SwitchSense Technique for the Study of Small Molecules’ (Ethidium Bromide and Selected Sulfonamide Derivatives) Affinity to DNA in Real Time. J Phys Chem B 2022; 126:7238-7251. [PMID: 36106569 PMCID: PMC9527753 DOI: 10.1021/acs.jpcb.2c03138] [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] [Indexed: 11/29/2022]
Abstract
![]()
The discovery and introduction of the switchSense technique
in
the chemical laboratory have drawn well-deserved interest owing to
its wide range of applications. Namely, it can be used to determine
the diameter of proteins, alterations in their tertiary structures
(folding), and many other conformational changes that are important
from a biological point of view. The essence of this technique is
based on its ability to study of the interactions between an analyte
and a ligand in real time (in a buffer flow). Its simplicity, on the
other hand, is based on the use of a signaling system that provides
information about the ongoing interactions based on the changes in
the fluorescence intensity. This technique can be extremely advantageous
in the study of new pharmaceuticals. The design of compounds with
biological activity, as well as the determination of their molecular
targets and modes of interactions, is crucial in the search for new
drugs and the fight against drug resistance. This article presents
another possible application of the switchSense technique for the
study of the binding kinetics of small model molecules such as ethidium
bromide (EB) and selected sulfonamide derivatives with DNA in the
static and dynamic modes at three different temperatures (15, 25,
and 37 °C) each. The experimental results remain in very good
agreement with the molecular dynamics docking ones. These physicochemical
insights and applications obtained from the switchSense technique
allow for the design of an effective strategy for molecular interaction
assessments of small but pharmaceutically important molecules with
DNA.
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Affiliation(s)
- Sandra Ramotowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Paulina Spisz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Jakub Brzeski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | - Mariusz Makowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
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30
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Georgakopoulou C, Thomos D, Tsolis T, Ypsilantis K, Plakatouras JC, Kordias D, Magklara A, Kouderis C, Kalampounias AG, Garoufis A. Synthesis, characterization, interactions with the DNA duplex dodecamer d(5'-CGCGAATTCGCG-3') 2 and cytotoxicity of binuclear η 6-arene-Ru(II) complexes. Dalton Trans 2022; 51:13808-13825. [PMID: 36039685 DOI: 10.1039/d2dt02304k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The novel binuclear η6-arene-Ru(II) complexes with the general formula {[(η6-cym)Ru(L)]2(μ-BL)}(PF6)4, and their corresponding water soluble {[(η6-cym)Ru(L)]2(μ-BL)}Cl4, where cym = p-cymene, L = 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen), BL = 4,4'-bipyridine (BL-1), 1,2-bis(4-pyridyl)ethane (BL-2) and 1,3-bis(4-pyridyl)propane (BL-3), were synthesized and characterized. The structure of {[(η6-cym)Ru(phen)]2(μ-BL-1)}(PF6)4 was determined by X-ray single crystal methods. The interaction of {[(η6-cym)Ru(phen)]2(μ-BL-i)}Cl4 (i = 1, 2, 3; (4), (5) and (6) correspondingly) with the DNA duplex d(5'-CGCGAATTCGCG-3')2 was studied by means of NMR techniques and fluorescence titrations. The results show that complex (4) binds with a Kb = 12.133 × 103 M-1 through both intercalation and groove binding, while (5) and (6) are groove binders (Kb = 2.333 × 103 M-1 and Kb = 3.336 × 103 M-1 correspondingly). Comparison with the mononuclear complex [(η6-cym)Ru(phen)(py)]2+ reveals that it binds to the d(5'-CGCGAATTCGCG-3')2 with a Kb value two orders of magnitude lower than (4) (Kb = 0.158 × 103 M-1), indicating that for the binuclear complexes both ruthenium moieties participate in the binding. The complexes were found to be cytotoxic against the A2780 and A2780 res. cancer cell line with a selectivity index (SI) in the range of 3.0-5.9.
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Affiliation(s)
| | - Dimitrios Thomos
- Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece.
| | - Theodoros Tsolis
- Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece.
| | | | - John C Plakatouras
- Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece. .,University Research Center of Ioannina (URCI), Institute of Materials Science and Computing, Ioannina, Greece
| | - Dimitris Kordias
- Biomedical Research Institute-Foundation for Research and Technology, 45110 Ioannina, Greece.,Laboratory of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Angeliki Magklara
- Biomedical Research Institute-Foundation for Research and Technology, 45110 Ioannina, Greece.,Laboratory of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece.,Institute of Biosciences, University Research Center of Ioannina (U.R.C.I.), Ioannina, Greece
| | | | - Angelos G Kalampounias
- Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece. .,University Research Center of Ioannina (URCI), Institute of Materials Science and Computing, Ioannina, Greece
| | - Achilleas Garoufis
- Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece. .,University Research Center of Ioannina (URCI), Institute of Materials Science and Computing, Ioannina, Greece
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31
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Zhang A, Kondhare D, Leonard P, Seela F. Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration. Chemistry 2022; 28:e202201294. [PMID: 35652726 PMCID: PMC9543212 DOI: 10.1002/chem.202201294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/15/2022]
Abstract
DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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32
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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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33
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Hussein Ali T, Mousa Mandal A, Alhasan A, Dehaen W. Surface fabrication of magnetic core-shell silica nanoparticles with perylene diimide as a fluorescent dye for nucleic acid visualization. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Galindo-Murillo R, Cheatham TE. Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA. J Phys Chem Lett 2022; 13:6283-6287. [PMID: 35775742 PMCID: PMC9466961 DOI: 10.1021/acs.jpclett.2c01348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Duplex DNA is modeled as canonical B-DNA displaying the characteristic Watson-Crick base pairs. A less common and short-lived pairing of the nucleobases is the Hoogsteen (HG) conformation. The low population of the HG base pairs (<1%) necessitates extended sampling times in order to analyze through unbiased molecular dynamics (MD) simulations. We have discovered that with extended sampling times using multiple independent copies of an 18-mer sequence, the MD trajectories reproduce the expected and transient HG base pairing. Consistent with experiment, the percentage of the HG events are within the range of ∼0.1-1.0% over the combined aggregate sampling time of more than 3.6 ms. We present the reliability of the current AMBER set of nucleic acid force fields and tools to accurately simulate naturally occurring base-pairing and opening events without any bias or restraints. The mechanism consists of base pair fraying, flipping of the purine, and reformation with HG base pairs.
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35
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Venugopal S, Sharma V, Anuradha M, Singh I, Singh G. DNA Intercalators as Anticancer Agents. Chem Biol Drug Des 2022; 100:580-598. [PMID: 35822451 DOI: 10.1111/cbdd.14116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/17/2022] [Accepted: 06/26/2022] [Indexed: 11/28/2022]
Abstract
Cancer is one of the most prevailing disease conditions which occurs due to uncontrolled cell division either due to natural mutation to the genes or due to changes induced by physical, chemical, or biological carcinogens. According to WHO, it is the second leading cause of death worldwide and has reported 10 million deaths in 2020. Hence there arises the need for better chemotherapies and DNA intercalators are one such emerging therapy for cancer. DNA intercalating agents reversibly intercalate with the double-helical structure of DNA by interacting with adjacent base pairs and disrupting the structure of DNA and thereby causing cell death. Here we discuss the different classes of organo-intercalators used in cancer therapy describing their anticancer and intercalation ability by different methods along with their structure-activity relationship and mechanism of action.
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Affiliation(s)
- Sneha Venugopal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Vikas Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Mehra Anuradha
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Iqubal Singh
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
| | - Gurdeep Singh
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Punjab-144411, India
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36
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Lisa John V, Joy F, Jose Kollannoor A, Joseph K, Nair Y, T. P. V. Amine functionalized carbon quantum dots from paper precursors for selective binding and fluorescent labelling applications. J Colloid Interface Sci 2022; 617:730-744. [DOI: 10.1016/j.jcis.2022.03.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 01/14/2023]
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37
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Huang G, Ma J, Li J, Yan L. Study on the interaction between aflatoxin M1 and DNA and its application in the removal of aflatoxin M1. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Pugsley CE, Isaac RE, Warren NJ, Behra JS, Cappelle K, Dominguez-Espinosa R, Cayre OJ. Protection of Double-Stranded RNA via Complexation with Double Hydrophilic Block Copolymers: Influence of Neutral Block Length in Biologically Relevant Environments. Biomacromolecules 2022; 23:2362-2373. [PMID: 35549247 PMCID: PMC9198985 DOI: 10.1021/acs.biomac.2c00136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Interaction between
the anionic phosphodiester backbone of DNA/RNA
and polycations can be exploited as a means of delivering genetic
material for therapeutic and agrochemical applications. In this work,
quaternized poly(2-(dimethylamino)ethyl methacrylate)-block-poly(N,N-dimethylacrylamide) (PQDMAEMA-b-PDMAm) double hydrophilic block copolymers
(DHBCs) were synthesized via reversible addition–fragmentation
chain-transfer (RAFT) polymerization as nonviral delivery vehicles
for double-stranded RNA. The assembly of DHBCs and dsRNA forms distinct
polyplexes that were thoroughly characterized to establish a relationship
between the length of the uncharged poly(N,N-dimethylacrylamide)
(PDMA) block and the polyplex size, complexation efficiency, and colloidal
stability. Dynamic light scattering reveals the formation of smaller
polyplexes with increasing PDMA lengths, while gel electrophoresis
confirms that these polyplexes require higher N/P ratio for full complexation.
DHBC polyplexes exhibit enhanced stability in low ionic strength environments
in comparison to homopolymer-based polyplexes. In vitro enzymatic degradation assays demonstrate that both homopolymer and
DHBC polymers efficiently protect dsRNA from degradation by RNase
A enzyme.
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Affiliation(s)
- Charlotte E Pugsley
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom.,School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - R Elwyn Isaac
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nicholas J Warren
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Juliette S Behra
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Kaat Cappelle
- Syngenta Ghent Innovation Center, Technologiepark 30, B-9052 Gent-Zwijnaarde, Belgium
| | - Rosa Dominguez-Espinosa
- Syngenta Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, England
| | - Olivier J Cayre
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
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39
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DNA dyes: toxicity, remediation strategies and alternatives. Folia Microbiol (Praha) 2022; 67:555-571. [PMID: 35292916 DOI: 10.1007/s12223-022-00963-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/08/2022] [Indexed: 11/04/2022]
Abstract
Release of untreated effluent from processing or manufacturing industries and other commercial premises into water bodies is a major threat to environment and human health. In this regard, the effluent generated from laboratories and other research facilities is of great concern. Among other harmful chemicals, the effluent is rich in toxic organic dyes, which get exposed to the environment and pose serious health risk. The dyes used in nucleic acid analysis specially the DNA dyes are known for their teratogenicity and mutagenic potential, which mainly depends upon the organism and circumstances under which it is exposed. Among animals and humans, exposure to theses dyes may lead to irritation in mouth, eyes and respiratory tract and many other possible effects which are yet to be explored. To overcome these problems, dyes present in the effluents from laboratories must be degraded to non-toxic forms. Various strategies have been proposed and investigated for degradation and remediation of contaminated laboratory effluent. As a modern and cost-effective technique, biodegradation using microbes and plants is potentially eco-friendly and sustainable technique for detoxifying these dyes. In this article, we have discussed and reviewed the structure, properties and toxicity profile of prominent nucleic acid dyes, along with the strategies of remediation of laboratory effluents contaminated with these dyes. In addition, we have also discussed the feasibility and limitations of these remediation strategies and identified research gaps that can help researchers to explore more effective solutions to manage this area of great concern. We have also reviewed various less toxic alternatives of these common as safer options of these dyes.
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40
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Pronkin PG, Tatikolov AS. Meso-aryl-substituted thiacarbocyanine dyes as spectral-fluorescent probes for DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120744. [PMID: 34929626 DOI: 10.1016/j.saa.2021.120744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The noncovalent interaction of meso-aryl-substituted thiacarbocyanine dyes I and II with dsDNA and ssDNA in aqueous solutions has been studied by spectral-fluorescent methods. Complexation with DNA is accompanied by both aggregation of the dyes and the formation of monomeric strongly fluorescent complexes. Experiments on molecular docking of dyes I and II with dsDNA confirm the previous assumption about the possibility of the formation of complexes of different types: intercalation between base pairs and in the grooves of the double helix of the biopolymer. The possibility of intercalation of the dyes in the complex is confirmed by experiments on thermal dissociation of dsDNA in the presence of dyes I and II, as well as experiments on the interaction of the dyes with ssDNA. An increase in the melting temperatures Tm of dsDNA is obtained in the presence of I and II, similar to that observed for the classical intercalator ethidium bromide. The limits of detection and quantification of DNA, which are important for the use of the dyes as probes for DNA, have been determined. The primary photochemical processes of the dyes in complexes with ssDNA were studied by flash photolysis technique. Complexation with ssDNA hinders photoisomerization and creates favorable conditions for the dye triplet state formation. The decay kinetics of the triplet state of the dyes were monoexponential. The rate constant of quenching of the triplet state by air oxygen was estimated for dye I complexed with ssDNA and was found to be less than the diffusion-controlled limit. This is probably a consequence of the shielding effect of the complex on the triplet quenching process.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
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41
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Khursheed S, Tabassum S, Arjmand F. Comprehensive biological {DNA/RNA binding profile, cleavage &cytotoxicity activity} of structurally well-characterized chromone-appended Cu(II)(L1-3)(phen) potential anticancer drug candidates. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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42
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Nickel (II), copper (II), and vanadyl (II) complexes with tridentate nicotinoyl hydrazone derivative functionalized as effective catalysts for epoxidation processes and as biological reagents. J Taiwan Inst Chem Eng 2022. [DOI: 10.1016/j.jtice.2021.104192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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43
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Das A, Banik BK. Advances in heterocycles as DNA intercalating cancer drugs. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The insertion of a molecule between the bases of DNA is known as intercalation. A molecule is able to interact with DNA in different ways. DNA intercalators are generally aromatic, planar, and polycyclic. In chemotherapeutic treatment, to suppress DNA replication in cancer cells, intercalators are used. In this article, we discuss the anticancer activity of 10 intensively studied DNA intercalators as drugs. The list includes proflavine, ethidium bromide, doxorubicin, dactinomycin, bleomycin, epirubicin, mitoxantrone, ellipticine, elinafide, and echinomycin. Considerable structural diversities are seen in these molecules. Besides, some examples of the metallo-intercalators are presented at the end of the chapter. These molecules have other crucial properties that are also useful in the treatment of cancers. The successes and limitations of these molecules are also presented.
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Affiliation(s)
- Aparna Das
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
| | - Bimal Krishna Banik
- Department of Mathematics and Natural Sciences , College of Sciences and Human Studies, Prince Mohammad Bin Fahd University , Al Khobar 31952 , Kingdom of Saudi Arabia
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44
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Mohan N, Vidhya CV, Suni V, Mohamed Ameer J, Kasoju N, Mohanan PV, Sreejith SS, Prathapachandra Kurup MR. Copper( ii) salen-based complexes as potential anticancer agents. NEW J CHEM 2022. [DOI: 10.1039/d2nj02170f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The systematic design and synthesis of four Cu(ii) salen compounds and their potential as excellent anticancer agents is discussed using biological studies.
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Affiliation(s)
- Nithya Mohan
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala-682 022, India
| | - C. V. Vidhya
- Department of Chemistry, National Institute of Technology Calicut, NIT Campus 673 601, Kerala, India
| | - V. Suni
- Department of Chemistry, National Institute of Technology Calicut, NIT Campus 673 601, Kerala, India
| | - Jimna Mohamed Ameer
- Division of Tissue Culture, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695012, India
| | - Naresh Kasoju
- Division of Tissue Culture, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695012, India
| | - P. V. Mohanan
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala-682 022, India
| | - S. S. Sreejith
- Department of Chemical Oceanography, Cochin University of Science and Technology, Kochi 682 022, Kerala, India
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45
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Pugsley CE, Isaac RE, Warren NJ, Cayre OJ. Linear ABC amphiphilic triblock copolymers for complexation and protection of dsRNA. Polym Chem 2022. [DOI: 10.1039/d2py00914e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We herein report the synthesis and characterisation of linear ABC triblock copolymers, investigation of their self-assembly in aqueous solution, and complexation with and protection of double stranded-RNA (dsRNA).
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Affiliation(s)
- Charlotte E. Pugsley
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - R. Elwyn Isaac
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicholas J. Warren
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Olivier J. Cayre
- School of Chemical and Process Engineering, University of Leeds, Leeds, LS2 9JT, UK
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46
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Pronkin PG, Tatikolov AS. Photonics of meso-substituted carbocyanine dyes in solutions and in complexes with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 263:120171. [PMID: 34280796 DOI: 10.1016/j.saa.2021.120171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Spectral-fluorescent and photochemical properties (photoisomerization and generation of the triplet state) of meso-substituted cationic carbocyanine dyes, 3,3'-di-(β-hydroxyethyl)-5,5'-dimethoxy-9-ethylthiacarbocyanine iodide (K1) and 3,3'-di-(β-hydroxyethyl)-9-methylthiacarbocyanine iodide (K2), have been studied in solutions and in the presence of DNA. In solutions, on passing from acetonitrile to dioxane, a growth of fluorescence of the dyes is observed due to a shift of the equilibrium of cis/trans isomers toward the fluorescent trans-isomer. Upon flash photolysis of dye solutions in dioxane, the formation and subsequent decay of the cis-photoisomers of the dyes are observed. In aqueous solutions, the interaction with DNA leads to the formation of noncovalent complexes of K1 and K2 with DNA, which is accompanied by a significant increase in the fluorescence intensity. The results of the molecular docking experiments showed the possibility of several types of binding, which was confirmed by the data obtained from other experiments. The effects of temperature and additions of NaCl on the stability of the dye-DNA complexes were studied. The spectral-fluorescent data were used to estimate the binding constants of the dyes with DNA and other characteristics of the dyes that are important for their use as probes. Upon flash photolysis of the dyes in complexes with DNA, photoisomerization is not observed, but the quantum yield of intersystem crossing to the triplet state increases. The decay of the triplet states occurs by a two-exponential law. The rate constants for quenching of the triplet states of the dyes complexed with DNA by oxygen were found to be lower than the expected values for diffusion-controlled quenching (taking into account the spin statistical factor 1/9), which is explained by the steric factor of complexation.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
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Dayanidhi PD, Vaidyanathan VG. Understanding the ancillary ligand effect on luminescent cyclometalated Ir(III) complex as a reporter for 2-acetylaminofluorene DNA(AAF-dG) adduct. J Biol Inorg Chem 2021; 27:189-199. [PMID: 34843001 DOI: 10.1007/s00775-021-01920-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022]
Abstract
Mutagenic agents such as aromatic amines undergo metabolic activation and produce DNA adducts at C8 position of guanine bases. N-2-acetylaminofluorene (AAF) generates different mutational outcomes when placed at G1, G2, and G3 of a NarI sequence (-G1G2CG3CC/T-). These outcomes are dictated by the conformations adopted by these adducts. Detection of such lesions is of considerable interest owing to their hazardous effects. Here, we report the synthesis of three cyclometalated [Ir(L)2dppz]+ complexes (L = 2-phenylpyridine (ppy) 1; benzo[h]quinoline (bhq) 2; 2-phenylquinoline (pq) 3; dppz = dipyrido[3,2-a:2',3'-c]phenazine) and their interaction with AAF adducted NarI DNA. Remarkably, complexes 1 and 2 displayed dominant 3LC transition characteristic of polar environment despite binding to the adducted sites. On the other hand, complex 3 binds to NarI sequences and behaves as a luminescent reporter for AAF-modified DNA. The results reported here emphasize that molecular light switching phenomenon can be stimulated by switching ancillary ligands and might act as potential probes for covalent-DNA defects.
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Affiliation(s)
- P David Dayanidhi
- Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - V G Vaidyanathan
- Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Zhang C, Xue Y, Wang L, Wu Q, Fang B, Sheng Y, Bai H, Peng B, Yang N, Li L. Progress on the Physiological Function of Mitochondrial DNA and Its Specific Detection and Therapy. Chembiochem 2021; 23:e202100474. [PMID: 34661371 DOI: 10.1002/cbic.202100474] [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: 09/05/2021] [Revised: 10/16/2021] [Indexed: 11/10/2022]
Abstract
Mitochondrial DNA (mtDNA) is the genetic information of mitochondrion, and its structure is circular double-stranded. Despite the diminutive size of the mitochondrial genome, mtDNA mutations are an important cause of mitochondrial diseases which are characterized by defects in oxidative phosphorylation (OXPHOS). Mitochondrial diseases are involved in multiple systems, particularly in the organs that are highly dependent on aerobic metabolism. The diagnosis of mitochondrial disease is more complicated since mtDNA mutations can cause various clinical symptoms. To realize more accurate diagnosis and treatment of mitochondrial diseases, the detection of mtDNA and the design of drugs acting on it are extremely important. Over the past few years, many probes and therapeutic drugs targeting mtDNA have been developed, making significant contributions to fundamental research including elucidation of the mechanisms of mitochondrial diseases at the genetic level. In this review, we summarize the structure, function, and detection approaches for mtDNA. The most current topics in this field, such as mechanistic exploration and treatment of mtDNA mutation-related disorders, are also reviewed. Specific attention is given to discussing the design and development of these probes and drugs for mtDNA. We hope that this review will provide readers with a comprehensive understanding of the importance of mtDNA, and promote the development of effective molecules for theragnosis of mtDNA mutation-related diseases.
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Affiliation(s)
- Congcong Zhang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Yufei Xue
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Lan Wang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Bin Fang
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Yu Sheng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Naidi Yang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China.,The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, Fujian, P. R. China
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