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Pundir M, De Rosa MC, Lobanova L, Abdulmawjood S, Chen X, Papagerakis S, Papagerakis P. Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders. Anal Chim Acta 2023; 1251:340971. [PMID: 36925277 DOI: 10.1016/j.aca.2023.340971] [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: 11/14/2022] [Revised: 01/25/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate dim light melatonin onset (established indicator of circadian rhythm sleep disorders) measurement requires lengthy assays, and antibody affinities alterations, especially in patients with circadian rhythm disorders whose melatonin salivary levels vary significantly, making antibodies detection mostly inadequate. In contrast, aptamers with their numerous advantages (e.g., target selectivity, structural flexibility in tuning binding affinities, small size, etc.) can become preferable biorecognition molecules for salivary melatonin detection with high sensitivity and specificity. This study thoroughly characterizes the structural property and binding mechanism of a single-stranded DNA aptamer full sequence (MLT-C-1) and its truncated versions (MLT-A-2, MLT-A-4) to decipher its optimal characteristics for saliva melatonin detection. We use circular dichroism spectroscopy to determine aptamers' conformational changes under different ionic strengths and showed that aptamers display a hairpin loop structure where few base pairs in the stem play a significant role in melatonin binding and formation of aptamer stabilized structure. Through microscale thermophoresis, aptamers demonstrated a high binding affinity in saliva samples (MLT-C-1F Kd = 12.5 ± 1.7 nM; MLT-A-4F Kd = 11.2 ± 1.6 nM; MLT-A-2F Kd = 2.4 ± 2.8 nM; limit-of-detection achieved in pM, highest sensitivity attained for MLT-A-2F aptamer with the lowest detection limit of 1.35 pM). Our data suggest that aptamers are promising as biorecognition molecules and provide the baseline parameters for the development of an aptamer-based point-of-care diagnostic system for melatonin detection and accurate profiling of its fluctuations in saliva.
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Affiliation(s)
- Meenakshi Pundir
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Maria C De Rosa
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada.
| | - Liubov Lobanova
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Shahad Abdulmawjood
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Xiongbiao Chen
- Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Department of Mechanical Engineering, School of Engineering, University of Saskatchewan, 57 Campus Dr, S7K 5A9, Saskatoon, Canada.
| | - Silvana Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, 48109, United States.
| | - Petros Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada.
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2
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Tian Z, Ding T, Niu H, Mu Y, Xu N, Kong M, Zhang Y, Tian Z, Wu Y, Wang C. The substituent group effect: investigation of naphthalimide-spermidine conjugates binding to DNA by spectroscopy, molecular docking and dynamics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Zhang H, Zhang X, Huang G, Li F, Wu F, Xie C, Liu D, Yao D. Screening ssDNA Aptamers Against Human Vascular Endothelial Factor 165 via Semirational Design. J Chem Inf Model 2022; 62:4983-4991. [PMID: 36215718 DOI: 10.1021/acs.jcim.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a valid tumor marker, vascular endothelial growth factor 165 (VEGF165) is an effective therapeutic target for anticancer treatments. Aptamers hold great promise for the development of anti-VEGF strategies. In this study, anti-VEGF165 ssDNA aptamers were screened using a semirational design and a multilevel screening strategy. Recombinant human VEGF165 protein was used as a target for the construction of an ssDNA virtual aptamer library with ssDNA that had one sole secondary structure. After silicon-assisted prescreening, circular dichroism and isothermal titration calorimetry were used to further screen for candidates. Three aptamers (nos. 524, 529, and 64) with one sole secondary and tertiary structure, showing a high affinity for VEGF165, were identified. The KD values obtained using surface plasmon resonance analysis were 36.3, 288, and 79.3 nM for aptamers 524, 529, and 64, respectively. Cytological tests revealed that the three aptamers inhibit rhVEGF165-induced proliferation of HUVECs. Specifically, aptamer 529 had the strongest inhibitory effect (nearly 100% inhibition). The screening strategy used in our study showed improved screening efficiency relative to other methods and resulted in aptamers with one sole conformation. The aptamers had an advantage in ensuring the uniqueness of aptamer targeting. This semirational design and multilevel screening strategy provide a reference for the screening of other aptamers.
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Affiliation(s)
- Haiyi Zhang
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiyao Zhang
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Guanhong Huang
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Feifei Li
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Fengmei Wu
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Chunfang Xie
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Daling Liu
- Biotechnology Department, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Dongsheng Yao
- Institute of Biomedicine Jinan University, Guangzhou 510632, China.,National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou 510632, China.,Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
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4
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Kloczewiak M, Banks JM, Jin L, Brader ML. A Biopharmaceutical Perspective on Higher-Order Structure and Thermal Stability of mRNA Vaccines. Mol Pharm 2022; 19:2022-2031. [PMID: 35715255 PMCID: PMC9257798 DOI: 10.1021/acs.molpharmaceut.2c00092] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/27/2022]
Abstract
Preservation of the integrity of macromolecular higher-order structure is a tenet central to achieving biologic drug and vaccine product stability toward manufacturing, distribution, storage, handling, and administration. Given that mRNA lipid nanoparticles (mRNA-LNPs) are held together by an intricate ensemble of weak forces, there are some intriguing parallels to biologic drugs, at least at first glance. However, mRNA vaccines are not without unique formulation and stabilization challenges derived from the instability of unmodified mRNA and its limited history as a drug or vaccine. Since certain learning gained from biologic drug development may be applicable for the improvement of mRNA vaccines, we present a perspective on parallels and contrasts between the emerging role of higher-order structure pertaining to mRNA-LNPs compared to pharmaceutical proteins. In a recent publication, the location of mRNA encapsulated within lipid nanoparticles was identified, revealing new insights into the LNP structure, nanoheterogeneity, and microenvironment of the encapsulated mRNA molecules [Brader et al. Biophys. J. 2021, 120, 2766]. We extend those findings by considering the effect of encapsulation on mRNA thermal unfolding with the observation that encapsulation in LNPs increases mRNA unfolding temperatures.
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Affiliation(s)
- Marek Kloczewiak
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Jessica M. Banks
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Lin Jin
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Mark L. Brader
- Moderna, Inc., 200 Technology Square, Cambridge, Massachusetts 02139, United States
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5
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Goswami S, Ghosh R, Prasanthan P, Kishore N. Mode of interaction of altretamine with calf thymus DNA: biophysical insights. J Biomol Struct Dyn 2022; 41:3728-3740. [PMID: 35343872 DOI: 10.1080/07391102.2022.2054472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 103 M-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK-1 mol-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.
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Affiliation(s)
- Sathi Goswami
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Ritutama Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Pooja Prasanthan
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
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6
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Lighvan ZM, Khonakdar HA, Akbari A, Jahromi MD, Ramezanpour A, Kermagoret A, Heydari A, Jabbari E. Synthesis and biological evaluation of novel tetranuclear cyclopalladated complex bearing thiosemicarbazone scaffold ligand: Interactions with double‐strand DNA, coronavirus, and molecular modeling studies. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zohreh Mehri Lighvan
- Department of Polymer Processing Iran Polymer and Petrochemical Institute Tehran Iran
| | - Hossein Ali Khonakdar
- Department of Polymer Processing Iran Polymer and Petrochemical Institute Tehran Iran
- Leibniz‐Institut für Polymerforschung Dresdene. V Dresden Germany
| | - Ali Akbari
- Solid Tumor Research Center, Cellular and Molecular Medicine Research Institute Urmia University of Medical Sciences Urmia Iran
| | | | - Azar Ramezanpour
- Department of Chemistry Isfahan University of Technology Isfahan Iran
| | | | - Abolfazl Heydari
- Polymer Institute of the Slovak Academy of Sciences Bratislava Slovakia
| | - Esmaiel Jabbari
- Department of Chemical Engineering University of South Carolina Columbia South Carolina USA
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7
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Carloni LE, Wechselberger R, De Vijlder T. Characterization of In Vitro G-Quadruplex Formation of Imetelstat Telomerase Inhibitor. Nucleic Acid Ther 2021; 31:341-350. [PMID: 34018844 DOI: 10.1089/nat.2020.0918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Imetelstat (GRN163L) is a potent and specific telomerase inhibitor currently in clinical development for the treatment of hematological malignancies such as myelofibrosis and myelodysplastic syndrome. It is a 13-mer N3'-P5' thio-phosphoramidate oligonucleotide covalently functionalized at the 5'-end with a palmitoyl lipid moiety through an aminoglycerol linker. As a competitive inhibitor of human telomerase, imetelstat directly binds to the telomerase RNA component sequence (hTR) in the catalytic site of the enzyme and acts as a direct competitor of human telomere binding. Administration of imetelstat causes progressive shortening of the telomeres, thereby inhibiting malignant cells' proliferation. We report here the ability of imetelstat to form stable, parallel, intermolecular G-quadruplex structures in vitro. The impact of the ionic environment on the formation and stability of imetelstat higher-order structure was investigated through circular dichroism spectroscopy, thermal denaturation analysis, and size-exclusion chromatography. We demonstrated that different structural elements, such as the 5'-palmitoyl linker and the thio-phosphoramidate backbone, critically contribute to G-quadruplex stability. Experiments further showed that G-quadruplex formation does not hamper binding to the hTR oligonucleotide sequence in vitro.
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Affiliation(s)
- Laure-Elie Carloni
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
| | - Rainer Wechselberger
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
| | - Thomas De Vijlder
- Small Molecule Pharmaceutical Development, Janssen Research & Development, Beerse, Belgium
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8
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Huang G, Ma J, Li J, Yan L. Removal of 1,2-benzanthracene via the intercalation of 1,2-benzanthracene with DNA and magnetic bead-based separation. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 40:137-156. [PMID: 33124510 DOI: 10.1080/15257770.2020.1839905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this study, DNA-functionalize-magnetic beads were investigated as sorbent materials for effective removing 1,2-benzanthracene (BaA) from water. In order to reveal the removal mechanism, the interaction mode between BaA and DNA was evaluated by using various characterization tools such as UV-visible and circular dichroism spectroscopy, fluorescence and resonance scattering spectroscopy, and agarose gel electrophoresis. In the presence of BaA, the melting temperature of DNA increased from 76.2 °C to 82.3 °C, which closely related to the intercalating of BaA. It was found that a part of the ethidium bromide (EB) binding sites to DNA were occupied by BaA in EB competing study. The results indicated that a new complex appeared between hsDNA and BaA, and the number of the binding sites (n) and the binding constants (KA) at different temperatures were obtained. DNA binding saturation value (≈0.80) was obtained by resonance scattering spectra study. BaA could be enriched and removed by DNA-functionalize-magnetic beads via the intercalation, and the removal efficiency was 97.73% when the initial concentration was 2.45 x10-6 mol·L-1 (559.31 μg/L).
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Affiliation(s)
- Guoxia Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, Guangxi, P. R. China
| | - Ji Ma
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, Guangxi, P. R. China
| | - Junsheng Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, Guangxi, P. R. China
| | - Liujuan Yan
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou, Guangxi, P. R. China
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Parveen S, Arjmand F, Zhang Q, Ahmad M, Khan A, Toupet L. Molecular docking, DFT and antimicrobial studies of Cu(II) complex as topoisomerase I inhibitor. J Biomol Struct Dyn 2020; 39:2092-2105. [PMID: 32174234 DOI: 10.1080/07391102.2020.1743365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Herein, we report the synthesis and single crystal X-ray structure of Cu(II)-picolinic acid complex, 1 as a potent topoisomerase I inhibitor. The complex 1 crystallized in the triclinic crystal system with space group P-1. Comparative in vitro binding studies of complex 1 with CT DNA and tRNA were carried out revealing an electrostatic binding mode with higher binding propensity towards tRNA. The intrinsic bonding constant value, Kb was calculated to be 4.36 × 104 and 8.78 × 104 M-1 with CT DNA and tRNA respectively. DNA cleavage activity was carried out with a pBR322 plasmid DNA substrate to ascertain the cleaving ability. Furthermore, Topo-I inhibition assay of complex 1, performed via gel electrophoresis revealed a significant inhibitory effect on the enzyme catalytic activity at a minimum concentration of 15 µM. The DFT studies were carried out to provide better insight in the electronic transitions observed in the absorption spectrum of the complex 1. Molecular docking studies were carried out with DNA, RNA and Topo-I to determine the specific binding preferences at the target site and complement the spectroscopic studies. The antimicrobial potential of complex 1 was screened against E. coli, S. aureus, P. aeruginosa, B. subtilis and C. albicans; and compared with doxycycline, exhibiting an excellent maximum zone of inhibition of 28 mm against E. coli.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shazia Parveen
- Chemistry Department, Faculty of Science, Taibah University, Yanbu, Saudi Arabia.,Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Qianfan Zhang
- Chemistry Department, Brown University, Providence, RI, USA
| | - Musheer Ahmad
- Department of Applied Chemistry, Aligarh Muslim University, Aligarh, India
| | - Arif Khan
- Department of Chemistry, SCLS, Jamia Hamdard, Delhi, India
| | - Loic Toupet
- Institut de Physique de Rennes, UMR 625, Université de Rennes 1, Rennes Cedex, France
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10
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Zhang R, Zhang X, Jia C, Pan J, Liu R. Carbon black induced DNA damage and conformational changes to mouse hepatocytes and DNA molecule: A combined study using comet assay and multi-spectra methods. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 170:732-738. [PMID: 30583284 DOI: 10.1016/j.ecoenv.2018.12.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Carbon black (CB), a carbonaceous nanoparticle, has been widely applied in our daily lives and used as a typical model to study environmental safety and health impacts of airborne particles. Although the potential negative effects of CB to organisms have been reported a lot, very limited work is focused on the genotoxicity of CB on molecular and cellular level simultaneously. Herein, we investigated the interaction mechanism between CB and DNA molecule in depth by multiple spectra measurement, UV-vis absorption and ionic strength measurement. The fluorescence spectroscopy, ironic strength measurement and UV absorption indicated that CB changed the structure of DNA and interacted with DNA in an electrostatic binding mode. CD (circular dichroism) spectra proved no significant effects were caused by CB on the base stacking and helicity bands of DNA, which further verified that electrostatic binding is the main binding mode between CB and DNA. On the cellular level, the comet assay shows that CB exposure could cause a remarkable DNA strand break to the mouse hepatocytes after 24 co-incubation. This combined investigation suggests that CB could cause a serious genotoxicity both on molecular and cellular level.
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Affiliation(s)
- Rui Zhang
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Xun Zhang
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Chenhao Jia
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Jie Pan
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
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11
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Bollu A, Sharma NK. Tropolone-Conjugated DNA: Fluorescence Enhancement in the Duplex. Chembiochem 2019; 20:1467-1475. [PMID: 30677202 DOI: 10.1002/cbic.201800822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Indexed: 01/02/2023]
Abstract
Tropolone (2-hydroxycyclohepta-2,4,6-triene-1-one and tautomer) is a non-benzenoid bioactive natural chromophore with pH-dependent fluorescence character and extraordinary metal binding affinities, especially with transition-metal ions Cu2+ /Zn2+ /Ni2+ . This report describes the syntheses and biophysical studies of a new tropolonyl thymidine [(4(5)-hydroxy-5(4)-oxo-5(4)H-cyclohepta-1,3,6-trienyl)thymidine] (tr-T) nucleoside and of corresponding tropolone-conjugated DNA oligonucleotides that form B-form DNA duplex structures with a complementary DNA strand, although their duplex structures are less stable than that of the control. Furthermore, the stabilities of those DNA duplex structures are lowered by the presence of increasing numbers of tr-T residue or by decreasing pH of their environments. Most importantly, these duplex structures are made fluorescent because of the presence of the tropolone moieties conjugated to the thymidine residues. The fluorescence behavior of those duplex structures exhibits pH dependence, with stronger fluorescence at lower pH and weaker fluorescence at high pH. Importantly, the fluorescence characters of tr-DNA oligonucleotides are significantly enhanced by nearly threefold after duplex structure formation with their complementary control DNA oligonucleotide. Further, the fluorescence behavior of these tr-DNA duplex structures is also dependent on the pH conditions. Hence, tropolonyl-conjugated DNA represents a class of new fluorescent analogues that might be be employed for sensing DNA duplex formation and provide opportunities to improve fluorescence properties further.
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Affiliation(s)
- Amarnath Bollu
- School of Chemical Science, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, India
| | - Nagendra K Sharma
- School of Chemical Science, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai, India
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12
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Roudini L, NayebZadeh Eidgahi N, Rahimi HR, Saberi MR, Amiri Tehranizadeh Z, Beigoli S, Chamani J. Determining the interaction behavior of calf thymus DNA with berberine hydrochloride in the presence of linker histone: a biophysical study. J Biomol Struct Dyn 2019; 38:364-381. [DOI: 10.1080/07391102.2019.1574240] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Louisa Roudini
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Negar NayebZadeh Eidgahi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Hamid Reza Rahimi
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Modern Sciences & Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sima Beigoli
- Endoscopic and Minimally Invasive Surgery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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13
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Yousuf I, Usman M, Ahmad M, Tabassum S, Arjmand F. Single X-ray crystal structure, DFT studies and topoisomerase I inhibition activity of a tailored ionic Ag( i) nalidixic acid–piperazinium drug entity specific for pancreatic cancer cells. NEW J CHEM 2018; 42:506-519. [DOI: 10.1039/c7nj03602g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
DFT studies, Topo I inhibition assay and cytotoxic activity of novel ionic Ag(i) nalidixic acid–piperazinium molecular entity.
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Affiliation(s)
- Imtiyaz Yousuf
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Mohammad Usman
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Musheer Ahmad
- Department of Applied Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Sartaj Tabassum
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Farukh Arjmand
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
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14
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Tian Z, Cui H, Liu H, Dong J, Dong H, Zhao L, Li X, Zhang Y, Huang Y, Song L, Bian L, Wang Y, Xu X, Wang C. Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking. MEDCHEMCOMM 2017; 8:2079-2092. [PMID: 30108725 PMCID: PMC6072523 DOI: 10.1039/c7md00389g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/26/2017] [Indexed: 01/23/2023]
Abstract
The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Hailong Cui
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - He Liu
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Jun Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Huanyang Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Luyao Zhao
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xueting Li
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yan Zhang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yingying Huang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Lina Song
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Longxiang Bian
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Yuxia Wang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xuejun Xu
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
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15
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Upadhyay SK. Binding and thermodynamics of REV peptide-ctDNA interaction. Biopolymers 2017; 108. [PMID: 27353011 DOI: 10.1002/bip.22902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/13/2016] [Accepted: 06/25/2016] [Indexed: 02/04/2023]
Abstract
The thermodynamics of DNA-ligand binding is important as it provides useful information to understand the details of binding processes. HIV-1 REV response element (RRE) located in the env coding region of the viral genome is reported to be well conserved across different HIV-1 isolates. In this study, the binding characteristics of Calf thymus DNA (ctDNA) and REV peptide from HIV-1 were investigated using spectroscopic (UV-visible, fluorescence, and circular dichroism (CD)) and isothermal titration calorimetric (ITC) techniques. Thermal stability and ligand binding properties of the ctDNA revealed that native ctDNA had a Tm of 75.5 °C, whereas the ctDNA-REV peptide complex exhibited an incremental shift in the Tm by 8 °C, indicating thermal stability of the complex. CD data indicated increased ellipticity due to large conformational changes in ctDNA molecule upon binding with REV peptide and two binding stoichiometric modes are apparent. The ctDNA experienced condensation due to large conformational changes in the presence of REV peptide and positive B→Ψ transition was observed at higher molar charge ratios. Fluorescence studies performed at several ligand concentrations revealed a gradual decrease in the fluorescence intensity of EtBr-bound ctDNA in response to increasing ligand concentrations. The fluorescence data further confirmed two stoichiometric modes of binding for ctDNA-REV peptide complex as previously observed with CD studies. The binding enthalpies were determined using ITC in the temperature range of 293 K-308 K. The ITC binding isotherm was exothermic at all temperatures examined, with low ΔH values indicating that the ctDNA-REV peptide interaction is driven largely by entropy. The heat capacity change (ΔCp ) was insignificant, an unusual finding in the area of DNA-peptide interaction studies. The variation in the values obtained for ΔH, ΔS, and ΔG with temperature further suggests that ctDNA-REV peptide interaction is entropically driven. ITC based analysis of salt dependence of binding constant gave a charge value (Z) = +4.01, as determined for the δlnK/δln[Na+ ] parameter, suggesting the participation of only 3-4 Arg out of 11 Arg charge from REV peptide. The stoichiometry observed for the complex was three molar charge of REV peptide binding per molar charge of ctDNA. ITC based analysis further confirmed that the binding between ctDNA and REV peptide is governed by electrostatic interaction. Molecular interactions including H-bonding, van der Waals forces, and solvent molecules rearrangement, underlie the binding of REV peptide to ctDNA.
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16
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Tian Z, Zhao L, Dong H, Zhang Y, Zhang Y, Ren Q, Shao S, Huang Y, Song L, Guo T, Xu X, Wang C. Study on the interaction of anthracenyl-methyl homospermidine conjugate (ANTMHspd) with DNA by spectroscopic methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 169:27-34. [DOI: 10.1016/j.jphotobiol.2017.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/21/2017] [Indexed: 11/16/2022]
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17
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Ou Z, Xu M, Gao Y, Hu R, Li Q, Cai W, Wang Z, Qian Y, Yang G. Synthesis, G-quadruplex binding properties and cytotoxicity of naphthalimide–thiourea conjugates. NEW J CHEM 2017. [DOI: 10.1039/c7nj02366a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The hydrogen bonding between a thiourea moiety and a G-quadruplex plays a crucial role in the sequence-specific DNA binding of naphthalimide–thiourea conjugates.
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Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Moheng Xu
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Rui Hu
- CAS Key laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Qingqing Li
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Wenjiao Cai
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Ziji Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yimeng Qian
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Guoqiang Yang
- CAS Key laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
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18
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Effect of testosterone and its aliphatic and aromatic dimers on DNA morphology. Int J Biol Macromol 2016; 95:850-855. [PMID: 27693340 DOI: 10.1016/j.ijbiomac.2016.09.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023]
Abstract
Conjugation of DNA with testosterone and it aliphatic dimer (alip) and aromatic dimer (arom) was investigated in aqueous solution at pH 7.4. Multiple spectroscopic methods, transmission electron microscopy (TEM) and molecular modeling were used to characterize steroid-DNA binding and DNA morphology. Spectroscopic analysis showed that testosterone binds DNA via A7, A16, A17, T8, T15 and T18 nucleobases with overall binding constants Ktest-DNA=1.8 (±0.4)×104M-1, Ktest-dimeralip-DNA=5.7 (±0.7)×104M-1 and Ktest-dimer-arom-DNA=7.3 (±0.9)×104M-1. The binding affinity increases in this order: testosterone dimer-aromatic>testosterone dimer-aliphatic>testosterone. The steroid loading efficacy was 40-50%. Transmission electron microscopy showed major changes in DNA morphology as testosterone-DNA interaction occurred with increase in the diameter of the DNA aggregate, indicating encapsulation of testosterone by DNA. Modeling showed the presence of several nucleobases attached to testosterone with the free binding energy of -4.93Kcal/mol.
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19
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Biomolecular interaction, catecholase like activity and alkane oxidation in ionic liquids of a phenylcarbohydrazone-based monocopper(II) complex. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Parveen M, Ahmad F, Malla AM, Khan MS, Rehman SU, Tabish M, Silva MR, Silva PP. Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 159:218-28. [DOI: 10.1016/j.jphotobiol.2016.03.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 03/23/2016] [Accepted: 03/31/2016] [Indexed: 12/30/2022]
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21
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Review on the binding of anticancer drug doxorubicin with DNA and tRNA: Structural models and antitumor activity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:274-9. [PMID: 26971631 DOI: 10.1016/j.jphotobiol.2016.02.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/13/2016] [Indexed: 01/08/2023]
Abstract
In this review, we have compared the results of multiple spectroscopic studies and molecular modeling of anticancer drug doxorubicin (DOX) bindings to DNA and tRNA. DOX was intercalated into DNA duplex, while tRNA binding is via major and minor grooves. DOX-DNA intercalation is close to A-7, C-5, *C-19 (H-bonding with DOX NH2 group), G-6, T-8 and T-18 with the free binding energy of -4.99kcal/mol. DOX-tRNA groove bindings are near A-29, A-31, A-38, C-25, C-27, C-28, *G-30 (H-bonding) and U-41 with the free binding energy of -4.44kcal/mol. Drug intercalation induced a partial B to A-DNA transition, while tRNA remained in A-family structure. The structural differences observed between DOX bindings to DNA and tRNA can be the main reasons for drug antitumor activity. The results of in vitro MTT assay on SKC01 colon carcinoma are consistent with the observed DNA structural changes. Future research should be focused on finding suitable nanocarriers for delivery of DOX in vivo in order to exploit the full capacity of this very important anticancer drug.
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22
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Yousuf I, Arjmand F, Tabassum S, Toupet L, Khan RA, Siddiqui MA. Mechanistic insights into a novel chromone-appended Cu(II) anticancer drug entity: in vitro binding profile with DNA/RNA substrates and cytotoxic activity against MCF-7 and HepG2 cancer cells. Dalton Trans 2016; 44:10330-42. [PMID: 25970097 DOI: 10.1039/c5dt00770d] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new chromone-appended Cu(ii) drug entity () was designed and synthesized as a potential anticancer chemotherapeutic agent. The structural elucidation was carried out thoroughly by elemental analysis, FT-IR, EPR, ESI-MS and single crystal X-ray crystallography. Complex resulted from the in situ methoxylation reaction of the 3-formylchromone ligand and its subsequent complexation with the copper nitrate salt in a 2 : 1 ratio, respectively. crystallized in the monoclinic P21/c space group possessing the lattice parameters, a = 8.75 Å, b = 5.07 Å, c = 26.22 Å, α = γ = 90°, β = 96.3° per unit cell. Furthermore, in vitro interaction studies of with ct-DNA and tRNA were carried out which suggested more avid binding propensity towards the RNA target via intercalative mode, which was reflected from its Kb, K and Ksv values. The gel electrophoretic mobility assay was carried out on the pBR322 plasmid DNA substrate, to ascertain the cleaving ability and the mechanistic pathway in the presence of additives, and the results revealed the efficient cleaving ability of via the oxidative pathway. In vitro cell growth inhibition via the MTT assay was carried out to evaluate the cytotoxicity of complex and IC50 values were found to be in the range of 5-10 μg mL(-1) in HepG2 and MCF-7 cancer cell lines, which were found to be much lower than the IC50 values of previously reported similar Cu(ii) complexes. Additionally, in the presence of , reactive oxygen species (ROS) and thiobarbituric acid reactive substance (TBARS) levels in the tested cancer cell lines increased significantly, coupled with reduced glutathione (GSH) levels. Thus, our results suggested that ROS plays an important role in cell apoptosis induced by the Cu(ii) complex and validates its potential to act as a robust anticancer drug entity.
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Affiliation(s)
- Imtiyaz Yousuf
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
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23
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Tian Z, Huang Y, Zhang Y, Song L, Qiao Y, Xu X, Wang C. Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:1-15. [PMID: 26926663 DOI: 10.1016/j.jphotobiol.2016.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
Abstract
The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yingying Huang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Zhang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Lina Song
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Qiao
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; State Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuejun Xu
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
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24
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Ou Z, Qian Y, Gao Y, Wang Y, Yang G, Li Y, Jiang K, Wang X. Photophysical, G-quadruplex DNA binding and cytotoxic properties of terpyridine complexes with a naphthalimide ligand. RSC Adv 2016. [DOI: 10.1039/c6ra01441k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The complex3inhibits A549 cells selectively over non-cancerous NIH3T3 cells, which may correlate with its selective G-quadruplex binding and nuclear location.
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Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yimeng Qian
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunqing Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Guoqiang Yang
- CAS Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Yi Li
- Key Laboratory of Photochemical Convesion and Optoelectronic Material
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing
- People's Republic of China
| | - Kaiyue Jiang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Xin Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
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25
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Dey B, Mukherjee S, Mukherjee N, Mondal RK, Satpati B, Senapati D, Babu SPS. Green silver nanoparticles for drug transport, bioactivities and a bacterium (Bacillus subtilis)-mediated comparative nano-patterning feature. RSC Adv 2016. [DOI: 10.1039/c5ra27886d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Supramolecular hydrogel-capped non-toxic Ag NPs are effective for cellular drug transport and are potentially bioactive, which also leads to the formation of novel silver nanoparticles.
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Affiliation(s)
- B. Dey
- Department of Chemistry
- Visva-Bharati University
- Santiniketan 731235
- India
| | - S. Mukherjee
- Department of Zoology
- Visva-Bharati University
- Santiniketan 731235
- India
| | - N. Mukherjee
- Department of Zoology
- Visva-Bharati University
- Santiniketan 731235
- India
| | - R. K. Mondal
- Department of Chemistry
- Visva-Bharati University
- Santiniketan 731235
- India
| | - B. Satpati
- Surface Physics and Material Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - D. Senapati
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700064
- India
| | - S. P. Sinha Babu
- Department of Zoology
- Visva-Bharati University
- Santiniketan 731235
- India
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26
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Sharma S, Toupet L, Ahmad M, Arjmand F. Synthesis, characterization, and crystal structure of RNA targeted l- and d-phenylalanine-(1,10-phen)–copper(ii) conjugate complexes: comparative in vitro RNA binding profile of enantiomers and their biological evaluation by morphological studies and antibacterial activity. RSC Adv 2016. [DOI: 10.1039/c6ra14503e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chiral Cu(ii) complexes targeting RNA showing morphological changes and Docking model.
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Affiliation(s)
- Surbhi Sharma
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Loic Toupet
- Institut de Physique de Rennes
- UMR 625
- Université de Rennes 1
- 35042 Rennes Cedex
- France
| | - Musheer Ahmad
- Department of Applied Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Farukh Arjmand
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
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27
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Xiao Y, Xu K, Wang Q, Xiong X, Huang Y, Li H. Synthesis, structure, and calf-thymus DNA binding of ternary fleroxacin–Cu(ii) complexes. RSC Adv 2016. [DOI: 10.1039/c6ra18971g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The interaction between the synthesized fleroxacin complexes and CT DNA was investigated.
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Affiliation(s)
- Ying Xiao
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Kailin Xu
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Qing Wang
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Xinnuo Xiong
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Yanmei Huang
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Hui Li
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
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28
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Agudelo D, Kreplak L, Tajmir-Riahi HA. tRNA conjugation with chitosan nanoparticles: An AFM imaging study. Int J Biol Macromol 2015; 85:150-6. [PMID: 26723249 DOI: 10.1016/j.ijbiomac.2015.12.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 02/06/2023]
Abstract
The conjugation of tRNA with chitosan nanoparticles of different sizes 15,100 and 200 kDa was investigated in aqueous solution using multiple spectroscopic methods and atomic force microscopy (AFM). Structural analysis showed that chitosan binds tRNA via G-C and A-U base pairs as well as backbone PO2 group, through electrostatic, hydrophilic and H-bonding contacts with overall binding constants of KCh-15-tRNA=4.1 (±0.60)×10(3)M(-1), KCh-100-tRNA=5.7 (±0.8)×10(3)M(-1) and KCh-200-tRNA=1.2 (±0.3)×10(4)M(-1). As chitosan size increases more stable polymer-tRNA conjugate is formed. AFM images showed major tRNA aggregation and particle formation occurred as chitosan concentration increased. Even though chitosan induced major biopolymer structural changes, tRNA remains in A-family structure.
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Affiliation(s)
- D Agudelo
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada
| | - L Kreplak
- Department of Physics and Atmospheric Science, Sir James Dunn Building Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H4R2, Canada
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, University of Québec at Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada.
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29
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Subastri A, Ramamurthy C, Suyavaran A, Lokeswara Rao P, Preedia Babu E, Hari Krishna K, Suresh Kumar M, Thirunavukkarasu C. Probing the interaction of troxerutin with transfer RNA by spectroscopic and molecular modeling. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 153:137-44. [DOI: 10.1016/j.jphotobiol.2015.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022]
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30
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Agudelo D, Kreplak L, Tajmir-Riahi HA. Microscopic and spectroscopic analysis of chitosan-DNA conjugates. Carbohydr Polym 2015; 137:207-213. [PMID: 26686122 DOI: 10.1016/j.carbpol.2015.09.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 08/31/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022]
Abstract
Conjugations of DNA with chitosans 15 kD (ch-15), 100 kD (ch-100) and 200 kD (ch-200) were investigated in aqueous solution at pH 5.5-6.5. Multiple spectroscopic methods and atomic force microscopy (AFM) were used to locate the chitosan binding sites and the effect of polymer conjugation on DNA compaction and particle formation. Structural analysis showed that chitosan-DNA conjugation is mainly via electrostatic interactions through polymer cationic charged NH2 and negatively charged backbone phosphate groups. As polymer size increases major DNA compaction and particle formation occurs. At high chitosan concentration major DNA structural changes observed indicating a partial B to A-DNA conformational transition.
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Affiliation(s)
- D Agudelo
- Department of Chemistry-Biochemistry and Physics, Université of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, Canada G9A 5H7
| | - L Kreplak
- Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie, University, Lord Dalhousie Drive, Halifax, NS, Canada B3H 4R2
| | - H A Tajmir-Riahi
- Department of Chemistry-Biochemistry and Physics, Université of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, Canada G9A 5H7.
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Structural modeling for DNA binding to antioxidants resveratrol, genistein and curcumin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 151:69-75. [DOI: 10.1016/j.jphotobiol.2015.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 01/07/2023]
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32
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N'soukpoé-Kossi CN, Bourassa P, Mandeville JS, Bekale L, Bariyanga J, Tajmir-Riahi HA. Locating the binding sites of antioxidants resveratrol, genistein and curcumin with tRNA. Int J Biol Macromol 2015; 80:41-7. [PMID: 26093317 DOI: 10.1016/j.ijbiomac.2015.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/03/2015] [Accepted: 06/06/2015] [Indexed: 12/26/2022]
Abstract
We located the binding sites of antioxidants resveratrol, genistein and curcumin on tRNA in aqueous solution at physiological conditions using constant tRNA concentration and various polyphenol contents. FTIR, UV-visible, CD spectroscopic methods and molecular modeling were used to determine polyphenol binding sites, the binding constant and the effects of polyphenol complexation on tRNA conformation and particle formation. Structural analysis showed that polyphenols bind tRNA via G-C and A-U base pairs through hydrophilic, hydrophobic and H-bonding contacts with overall binding constants of K(res-tRNA)=8.95(±0.80)×10(3) M(-1), K(gen-tRNA)=3.07(±0.5)×10(3) M(-1) and K(cur-tRNA)=1.55(±0.3)×10(4) M(-1). Molecular modeling showed the participation of several nucleobases in polyphenol-tRNA adduct formation with free binding energy of -4.43 for resveratrol, -4.26 kcal/mol for genistein and -4.84 kcal/mol for curcumin, indicating that the interaction process is spontaneous at room temperature. While tRNA remains in A-family structure, major biopolymer aggregation and particle formation occurred at high polyphenol contents.
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Affiliation(s)
- C N N'soukpoé-Kossi
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - P Bourassa
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - J S Mandeville
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - L Bekale
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7
| | - J Bariyanga
- Department of Chemistry, University of Hawaii-West O'ahu, 96-129 Ala Ike, Pearl City, HI 96782, USA
| | - H A Tajmir-Riahi
- Department of Chemistry-Physics, Université du Québec à Trois-Riviéres, C. P. 500v, Trois-Riviéres, Québec, Canada G9A 5H7.
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Ou Z, Feng Z, Liu G, Chen Y, Gao Y, Li Y, Wang X. Synthesis and G-Quadruplex-binding Properties of Cationic Platinum(II) Terpyridine Complexes Containing σ-Alkynyl Auxiliaries. CHEM LETT 2015. [DOI: 10.1246/cl.141045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Zhao Feng
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Guixia Liu
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Yongjie Chen
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, TIPC, CAS
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education, Department of Applied Chemistry, School of Science, Northwestern Polytechnical University
| | - Yi Li
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, TIPC, CAS
| | - Xuesong Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, TIPC, CAS
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34
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Bourassa P, Tajmir-Riahi H. Folic acid binds DNA and RNA at different locations. Int J Biol Macromol 2015; 74:337-42. [DOI: 10.1016/j.ijbiomac.2014.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 12/19/2022]
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35
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Arjmand F, Yousuf I, Zaidi Y, Toupet L. Crystal structure determination, spectroscopic characterization and biological profile of a tailored ionic molecular entity, Sn(iv) iminodiacetic acid–piperazinediium conjugate: in vitro DNA/RNA binding studies, Topo I inhibition activity, cytotoxic and systemic toxicity studies. RSC Adv 2015. [DOI: 10.1039/c4ra13718c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In vitro DNA/RNA binding studies and cytotoxic activity of complex 1 along with its in vivo systemic toxicity assay.
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Affiliation(s)
- Farukh Arjmand
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Imtiyaz Yousuf
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Yusra Zaidi
- Department of Zoology
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Loic Toupet
- Institut de Physique de Rennes
- UMR 625
- Université de Rennes 1
- 35042 Rennes, Cedex
- France
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36
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Dey B, Mondal RK, Mukherjee S, Satpati B, Mukherjee N, Mandal A, Senapati D, Sinha Babu SP. A supramolecular hydrogel for generation of a benign DNA-hydrogel. RSC Adv 2015. [DOI: 10.1039/c5ra19172f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A DNA-hydrogel, produced using calf-thymus DNA and a 2′,4′,6′-tri(4-pyridyl)pyridine based luminescent supramolecular hydrogel, can stabilize sunray mediated photochemically synthesized bio-compatible, luminous Ag-NPs.
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Affiliation(s)
- B. Dey
- Department of Chemistry
- Visva-Bharati University
- Santiniketan-731235
- India
| | - R. K. Mondal
- Department of Chemistry
- Visva-Bharati University
- Santiniketan-731235
- India
| | - S. Mukherjee
- Department of Zoology
- Visva-Bharati University
- Santiniketan-731235
- India
| | - B. Satpati
- Surface Physics and Material Science Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| | - N. Mukherjee
- Department of Zoology
- Visva-Bharati University
- Santiniketan-731235
- India
| | - A. Mandal
- Department of Chemistry
- Behala College
- Kolkata 700060
- India
| | - D. Senapati
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata-700064
- India
| | - S. P. Sinha Babu
- Department of Zoology
- Visva-Bharati University
- Santiniketan-731235
- India
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37
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Li X, Gorle AK, Ainsworth TD, Heimann K, Woodward CE, Grant Collins J, Richard Keene F. RNA and DNA binding of inert oligonuclear ruthenium(ii) complexes in live eukaryotic cells. Dalton Trans 2015; 44:3594-603. [DOI: 10.1039/c4dt02575j] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Oligonuclear polypyridylruthenium(ii) complexes show selectivity for the nucleus of eukaryotic cells with a considerable preference for the RNA-rich nucleolus.
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Affiliation(s)
- Xin Li
- School of Physical
- Environmental and Mathematical Sciences
- University of New South Wales
- Australian Defence Force Academy
- Canberra
| | - Anil K. Gorle
- School of Physical
- Environmental and Mathematical Sciences
- University of New South Wales
- Australian Defence Force Academy
- Canberra
| | - Tracy D. Ainsworth
- ARC Centre of Excellence for Coral Reef Studies
- James Cook University
- Townsville
- Australia
| | - Kirsten Heimann
- College of Marine & Environmental Sciences
- James Cook University
- Townsville
- Australia
- Centre for Biodiscovery and Molecular Development of Therapeutics
| | - Clifford E. Woodward
- School of Physical
- Environmental and Mathematical Sciences
- University of New South Wales
- Australian Defence Force Academy
- Canberra
| | - J. Grant Collins
- School of Physical
- Environmental and Mathematical Sciences
- University of New South Wales
- Australian Defence Force Academy
- Canberra
| | - F. Richard Keene
- Centre for Biodiscovery and Molecular Development of Therapeutics
- James Cook University
- Townsville
- Australia
- Department of Matter & Materials
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38
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N'soukpoé-Kossi C, Bourassa P, Mandeville J, Tajmir-Riahi H. Modelling of vitamin A binding to tRNA. J Pharm Biomed Anal 2014; 99:28-34. [DOI: 10.1016/j.jpba.2014.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/25/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
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39
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Bourassa P, Thomas TJ, Bariyanga J, Tajmir-Riahi HA. Breast anticancer drug tamoxifen and its metabolites bind tRNA at multiple sites. Int J Biol Macromol 2014; 72:692-8. [PMID: 25263468 DOI: 10.1016/j.ijbiomac.2014.09.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/07/2014] [Accepted: 09/08/2014] [Indexed: 12/17/2022]
Abstract
The binding sites of breast anticancer drug tamoxifen and its metabolites with tRNA were located by FTIR, CD, UV-visible, and fluorescence spectroscopic methods and molecular modeling. Structural analysis showed that tamoxifen and its metabolites bind tRNA at several binding sites with overall binding constants of K(tam-tRNA) = 5.2 (± 0.6) × 10(4) M(-1), K(4-hydroxytam-tRNA) = 6.5 ( ± 0.5) × 10(4) M(-1) and K(endox-tRNA) = 1.3 (± 0.2) × 10(4) M(-1). The number of binding sites occupied by drug molecules on tRNA were 1 (tamoxifen), 0.8 (4-hydroxitamoxifen) and 1.2 (endoxifen). Docking showed the participation of several nucleobases in drug-tRNA complexes with the free binding energy of -4.31 (tamoxifen), -4.45 (4-hydroxtamoxifen) and -4.38 kcal/mol (endoxifen). The order of binding is 4-hydroxy-tamoxifen > tamoxifen > endoxifen. Drug binding did not alter tRNA conformation from A-family structure, while biopolymer aggregation occurred at high drug concentration.
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Affiliation(s)
- P Bourassa
- Department of Chemistry-Physics, University of Québec in Trois-Rivières, C. P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - T J Thomas
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, and Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - J Bariyanga
- Division of Humanities: Math/Sciences, University of Hawaii-West O'ahu, 91-1001 Farrington Highway, Kapolei, HI 96707, USA
| | - H A Tajmir-Riahi
- Department of Chemistry-Physics, University of Québec in Trois-Rivières, C. P. 500, Trois-Rivières, Québec G9A 5H7, Canada.
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40
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Tetrameric ZBRK1 DNA binding domain has affinity towards cognate DNA in absence of zinc ions. Biochem Biophys Res Commun 2014; 450:283-8. [PMID: 24924633 DOI: 10.1016/j.bbrc.2014.05.104] [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: 05/12/2014] [Accepted: 05/23/2014] [Indexed: 11/22/2022]
Abstract
Zinc finger transcription regulatory proteins play crucial roles in cell-cycle regulation, DNA damage response and tumor genesis. Human ZBRK1 is a zinc-finger transcription repressor protein, which recognizes double helical DNA containing consensus sequences of 5'GGGXXXCAGXXXTTT3'. In the present study, we have purified recombinant DNA binding domain of ZBRK1, and studied binding with zinc ions and DNA, using biophysical techniques. The elution profile of the purified protein suggests that this ZBRK1 forms a homotetramer in solution. Dissociation and pull down assays also suggest that this domain forms a higher order oligomer. The ZBRK1-DNA binding domain acquires higher stability in the presence of zinc ions and DNA. The secondary structure of the ZBRK1-DNA complex is found to be significantly altered from the standard B-DNA conformation.
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41
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Locating the binding sites of antitumor drug tamoxifen and its metabolites with DNA. J Pharm Biomed Anal 2014; 95:193-9. [DOI: 10.1016/j.jpba.2014.02.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 02/17/2014] [Accepted: 02/27/2014] [Indexed: 11/20/2022]
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42
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Synthesis, crystal structure and antiproliferative activity of Cu(II) nalidixic acid–DACH conjugate: Comparative in vitro DNA/RNA binding profile, cleavage activity and molecular docking studies. Eur J Med Chem 2014; 81:76-88. [DOI: 10.1016/j.ejmech.2014.04.080] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 04/27/2014] [Accepted: 04/29/2014] [Indexed: 11/19/2022]
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43
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Agudelo D, Bourassa P, Bérubé G, Tajmir-Riahi HA. Intercalation of antitumor drug doxorubicin and its analogue by DNA duplex: Structural features and biological implications. Int J Biol Macromol 2014; 66:144-50. [DOI: 10.1016/j.ijbiomac.2014.02.028] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 11/15/2022]
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44
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Ozdemir A, Gursaclı RT, Tekinay T. Non-intercalative, deoxyribose binding of boric acid to calf thymus DNA. Biol Trace Elem Res 2014; 158:268-74. [PMID: 24652629 DOI: 10.1007/s12011-014-9924-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
The present study characterizes the effects of the boric acid binding on calf thymus DNA (ct-DNA) by spectroscopic and calorimetric methods. UV-Vis absorbance spectroscopy, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), isothermal titration calorimetry (ITC), and Fourier transform infrared (FT-IR) spectroscopy were employed to characterize binding properties. Changes in the secondary structure of ct-DNA were determined by CD spectroscopy. Sizes and morphologies of boric acid-DNA complexes were determined by transmission electron microscopy (TEM). The kinetics of boric acid binding to calf thymus DNA (ct-DNA) was investigated by isothermal titration calorimetry (ITC). ITC results revealed that boric acid exhibits a moderate affinity to ct-DNA with a binding constant (K a) of 9.54 × 10(4) M(-1). FT-IR results revealed that boric acid binds to the deoxyribose sugar of DNA without disrupting the B-conformation at tested concentrations.
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Affiliation(s)
- Ayse Ozdemir
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Bilkent, 06800, Turkey
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45
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Interaction of 6 mercaptopurine with calf thymus DNA--deciphering the binding mode and photoinduced DNA damage. PLoS One 2014; 9:e93913. [PMID: 24718609 PMCID: PMC3981731 DOI: 10.1371/journal.pone.0093913] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 03/10/2014] [Indexed: 11/23/2022] Open
Abstract
DNA is one of the major intracellular targets for a wide range of anticancer and antibiotic drugs. Elucidating the binding between small molecules and DNA provides great help in understanding drug-DNA interactions and in designing of new and promising drugs for clinical use. The ability of small molecules to bind and interfere with DNA replication and transcription provides further insight into how the drugs control the expression of genes. Interaction of an antimetabolite anticancer drug 6mercaptopurine (6MP) with calf thymus DNA was studied using various approaches like UV-visible spectroscopy, fluorescence spectroscopy, CD, viscosity and molecular docking. UV-visible spectroscopy confirmed 6MP-DNA interaction. Steady state fluorescence experiments revealed a moderate binding constant of 7.48×103 M−1 which was consistent with an external binding mode. Competitive displacement assays further confirmed a non-intercalative binding mode of 6MP which was further confirmed by CD and viscosity experiments. Molecular docking further revealed the minimum energy conformation (−119.67 kJ/mole) of the complex formed between DNA and 6MP. Hence, the biophysical techniques and in-silico molecular docking approaches confirmed the groove binding/electrostatic mode of interaction between 6MP and DNA. Further, photo induced generation of ROS by 6MP was studied spectrophotometrically and DNA damage was assessed by plasmid nicking and comet assay. There was a significant increase in ROS generation and consequent DNA damage in the presence of light.
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46
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Iida K, Nagasawa K. Macrocyclic Polyoxazoles as G-Quadruplex Ligands. CHEM REC 2013; 13:539-48. [DOI: 10.1002/tcr.201300015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Keisuke Iida
- Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
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47
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Tan BG, Vijgenboom E, Worrall JAR. Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans. Nucleic Acids Res 2013; 42:1326-40. [PMID: 24121681 PMCID: PMC3902906 DOI: 10.1093/nar/gkt902] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl–DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control.
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Affiliation(s)
- Benedict G Tan
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK and Molecular Biotechnology, Institute of Biology Leiden, Sylvius Laboratory, Leiden University, PO Box 9505, 2300 RA Leiden, The Netherlands
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48
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Yu S, Li MH, Choi SK, Baker JR, Larson RG. DNA condensation by partially acetylated poly(amido amine) dendrimers: effects of dendrimer charge density on complex formation. Molecules 2013; 18:10707-20. [PMID: 24005965 PMCID: PMC6271276 DOI: 10.3390/molecules180910707] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/29/2013] [Accepted: 08/30/2013] [Indexed: 12/05/2022] Open
Abstract
The ability of poly(amido amine) (or PAMAM) dendrimers to condense semiflexible dsDNA and penetrate cell membranes gives them great potential in gene therapy and drug delivery but their high positive surface charge makes them cytotoxic. Here, we describe the effects of partial neutralization by acetylation on DNA condensation using light scattering, circular dichroism, and single molecule imaging of dendrimer-DNA complexes combed onto surfaces and tethered to those surfaces under flow. We find that DNA can be condensed by generation-five (G5) dendrimers even when the surface charges are more than 65% neutralized, but that such dendrimers bind negligibly when an end-tethered DNA is stretched in flow. We also find that when fully charged dendrimers are introduced by flow to end-tethered DNA, all DNA molecules become equally highly coated with dendrimers at a rate that becomes very fast at high dendrimer concentration, and that dendrimers remain bound during subsequent flow of dendrimer-free buffer. These results suggest that the presence of dendrimer-free DNA coexisting with dendrimer-bound DNA after bulk mixing of the two in solution may result from diffusion-limited irreversible dendrimer-DNA binding, rather than, or in addition to, the previously proposed cooperative binding mechanism of dendrimers to DNA.
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Affiliation(s)
- Shi Yu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming-Hsin Li
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ronald G. Larson
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-734-936-0772; Fax: +1-734-763-0459
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49
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Agudelo D, Bourassa P, Beauregard M, Bérubé G, Tajmir-Riahi HA. tRNA binding to antitumor drug doxorubicin and its analogue. PLoS One 2013; 8:e69248. [PMID: 23922696 PMCID: PMC3726733 DOI: 10.1371/journal.pone.0069248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/06/2013] [Indexed: 12/16/2022] Open
Abstract
The binding sites of antitumor drug doxorubicin (DOX) and its analogue N-(trifluoroacetyl) doxorubicin (FDOX) with tRNA were located, using FTIR, CD, fluorescence spectroscopic methods and molecular modeling. Different binding sites are involved in drug-tRNA adducts with DOX located in the vicinity of A-29, A-31, A-38, C-25, C-27, C-28, G-30 and U-41, while FDOX bindings involved A-23, A-44, C-25, C-27, G-24, G-42, G-53, G-45 and U-41 with similar free binding energy (-4.44 for DOX and -4.41 kcal/mol for FDOX adducts). Spectroscopic results showed that both hydrophilic and hydrophobic contacts are involved in drug-tRNA complexation and FDOX forms more stable complexes than DOX with K DOX-tRNA=4.7 (± 0.5)× 10(4) M(-1) and K FDOX-tRNA=6.3 (± 0.7)× 10(4) M(-1). The number of drug molecules bound per tRNA (n) was 0.6 for DOX and 0.4 for FDOX. No major alterations of tRNA structure were observed and tRNA remained in A-family conformation, while biopolymer aggregation and particle formation occurred at high drug concentrations.
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Affiliation(s)
- Daniel Agudelo
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Philippe Bourassa
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Marc Beauregard
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
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Agarwal S, Jangir DK, Mehrotra R. Spectroscopic studies of the effects of anticancer drug mitoxantrone interaction with calf-thymus DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 120:177-82. [PMID: 23266050 DOI: 10.1016/j.jphotobiol.2012.11.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022]
Abstract
Mitoxantrone (MTX) (1,4-dihydroxy-5,8-bis[[2-[(2-hydroxyethyl)amino]ethyl]amino]-9,10-anthracenedione) is a synthetic antineoplastic drug, widely used as a potent chemotherapeutic agent in the treatment of various types of cancer. It is structurally similar to classical anthracyclines. Widespread interest in the anticancer agent mitoxantrone has arisen because of its apparent lower risk of cardio-toxic effects compared to the naturally occurring anthracyclines. In the present work, we investigated the interaction of mitoxantrone with DNA in the buffer solution at physiological pH using Fourier transform infrared (FTIR), UV-Visible absorption and circular dichroism spectroscopic techniques. FTIR analysis revealed the intercalation of mitoxantrone between the DNA base pairs along with its external binding with phosphate-sugar backbone. The binding constant calculated for mitoxantrone-DNA association was found to be 3.88×10(5)M(-1) indicating high affinity of drug with DNA double helix. Circular dichroism spectroscopic results suggest that there are no major conformational changes in DNA upon interaction with drug except some perturbations in native B-DNA at local level. The present work shows the capability of spectroscopic analysis to characterize the nature of drug-biomolecule complex and the effects of such interaction on the structure of biomolecule.
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Affiliation(s)
- Shweta Agarwal
- Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Marg, New Delhi 110012, India
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