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Zalieckas J, Greve MM, Bellucci L, Sacco G, Håkonsen V, Tozzini V, Nifosì R. Quantum sensing of microRNAs with nitrogen-vacancy centers in diamond. Commun Chem 2024; 7:101. [PMID: 38710926 DOI: 10.1038/s42004-024-01182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
Label-free detection of nucleic acids such as microRNAs holds great potential for early diagnostics of various types of cancers. Measuring intrinsic biomolecular charge using methods based on field effect has been a promising way to accomplish label-free detection. However, the charges of biomolecules are screened by counter ions in solutions over a short distance (Debye length), thereby limiting the sensitivity of these methods. Here, we measure the intrinsic magnetic noise of paramagnetic counter ions, such as Mn2+, interacting with microRNAs using nitrogen-vacancy (NV) centers in diamond. All-atom molecular dynamics simulations show that microRNA interacts with the diamond surface resulting in excess accumulation of Mn ions and stronger magnetic noise. We confirm this prediction by observing an increase in spin relaxation contrast of the NV centers, indicating higher Mn2+ local concentration. This opens new possibilities for next-generation quantum sensing of charged biomolecules, overcoming limitations due to the Debye screening.
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Affiliation(s)
- Justas Zalieckas
- Department of Physics and Technology, University of Bergen, Bergen, Norway.
| | - Martin M Greve
- Department of Physics and Technology, University of Bergen, Bergen, Norway
| | - Luca Bellucci
- Istituto Nanoscienze - CNR, Pisa, Italy
- Lab NEST Scuola Normale Superiore, Pisa, Italy
| | - Giuseppe Sacco
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Verner Håkonsen
- NTNU NanoLab, Norwegian University of Science and Technology, Trondheim, Norway
| | - Valentina Tozzini
- Istituto Nanoscienze - CNR, Pisa, Italy
- Lab NEST Scuola Normale Superiore, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), sezione Pisa, Pisa, Italy
| | - Riccardo Nifosì
- Istituto Nanoscienze - CNR, Pisa, Italy.
- Lab NEST Scuola Normale Superiore, Pisa, Italy.
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Farasati Far B, Naimi-Jamal MR, Daneshgar H, Rabiee N. Co-delivery of doxorubicin/sorafenib by DNA-decorated green ZIF-67-based nanocarriers for chemotherapy and hepatocellular carcinoma treatment. ENVIRONMENTAL RESEARCH 2023; 225:115589. [PMID: 36858304 DOI: 10.1016/j.envres.2023.115589] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Zeolitic imidazolate framework-67 (ZIF-67) has been decorated with natural biomaterials and DNA to develop a promising strategy and suitable and safe co-delivery platform for doxorubicin and sorafenib (DOX-SOR). FT-IR, XRD, FESEM, and TEM were used to characterize the modified MOFs. Combined Ginkgo biloba leaf extract and E. coli DNA were used as green decorations, and as environmentally-friendly methods to be developed, and DOX and SOR were attached to the porosity and on the surface of the MOFs. TEM and FESEM images demonstrated that the green MOFs were successfully synthesized for biomedical applications and showed their cubic structure. As a result of the nanocarrier-drug interactions, 59.7% and 60.2% of the drug payload were achieved with DOX and SOR, respectively. HEK-293, HT-29, and MCF-7 cells displayed excellent viability by decoration with DNA and Ginkgo biloba leaf extract at low and high concentrations (0.1 and 50 μg/mL), suggesting they could be used in biomedical applications. MTT assays demonstrated that the nanocarriers are highly biocompatible with normal cells and possess anticancer properties when applied to HT-29 and MCF-7 cells. As a result of Ginkgo biloba leaf extract and DNA modification, DOX-SOR release was prolonged and pH-sensitive (highest release at pHs 4.5 and 5.5). The internalization and delivery of the drug were also studied using a 2d fluorescence microscope, demonstrating that the drug was effectively internalized. Cell images showed NPs internalizing in MCF-7 cells, proving their efficacy as drug delivery systems.
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Affiliation(s)
- Bahareh Farasati Far
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Tehran, 1684611367, Iran
| | - Mohammad Reza Naimi-Jamal
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Tehran, 1684611367, Iran.
| | - Hossein Daneshgar
- Department of Inorganic Chemistry, Faculty of Chemistry and Petroleum Sciences, Shahid Beheshti University, P. O. Box 19839-63113, Tehran, Iran
| | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, New South Wales, 2109, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, 6150, Australia.
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Schrenková V, Para Kkadan MS, Kessler J, Kapitán J, Bouř P. Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution. Phys Chem Chem Phys 2023; 25:8198-8208. [PMID: 36880812 DOI: 10.1039/d2cp05756e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3' hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids.
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Affiliation(s)
- Věra Schrenková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Mohammed Siddhique Para Kkadan
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague, Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic. .,Department of Analytical Chemistry, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
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Aging hampers neutrophil extracellular traps (NETs) efficacy. Aging Clin Exp Res 2022; 34:2345-2353. [PMID: 35920993 PMCID: PMC9637667 DOI: 10.1007/s40520-022-02201-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/17/2022] [Indexed: 11/16/2022]
Abstract
Background NETosis is a neutrophil-mediated defense mechanism during which DNA and enzymes are extruded forming a network (NETs) trapping and killing different pathogens. NETosis is reduced in both mice and humans during aging. Aims We explored the difference in the efficacy of NETs released in elderly (> 65 years) versus adults (20–50 years) subjects in inhibiting Staphylococcus aureus growth and activating the growth of keratinocytes. Methods Neutrophil granulocytes, obtained from venous blood both in healthy elderly and adult subjects, were stimulated by LPS (0–250 µg/ml) to induce the formation of NET. NETs were quantified by SYBR Green staining and growth inhibition of S. aureus was evaluated by disk diffusion test. Furthermore, NETs (0–500 ng/ml) were added to immortalized human keratinocytes (HaCaT cells), and their proliferation was evaluated by MTT assay after 24 h. Finally, the DNA size of NETs was evaluated by flow cytometry after SYBR Green staining. Results Greater production of NETs was observed in elderly subjects than in adults, but these NETs showed reduced bactericidal capacity and HaCaT cells’ proliferation stimulation. The activities of the NETs are related to the size of the extruded DNA threads, and when NETs size was analyzed, DNA from elderly showed a higher size compared to that obtained by adults. Discussion Unexpected results showed aging-related NETs structural modification resulting in both a lower antimicrobial activity and keratinocyte proliferation stimulation compared to NETs obtained from adults. Conclusions The NETs DNA size observed in elderly subjects has not been previously reported and could be part of other pathogenic mechanisms observed in aging.
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Perets EA, Olesen KB, Yan ECY. Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5765-5778. [PMID: 35482888 DOI: 10.1021/acs.langmuir.2c00365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure-function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air-water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C-H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C-H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.
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Affiliation(s)
- Ethan A Perets
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kristian B Olesen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Elsa C Y Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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Tymchenko EE, Soldatova AA, Chikhirzhina EV, Polyanichko AM. Analysis of Changes in the Structure of DNA when Interacting with Platinum Coordination Compounds by IR Spectroscopy. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922010195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Chakraborty M, Mohanty M, Dinda R, Sengupta S, Kumar Chattopadhyay S. Cu(II) complexes of a bio-compatible aminoguanidine Schiff base: Histidine sensing and DNA-binding studies. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Haque S, Tripathy S, Patra CR. Manganese-based advanced nanoparticles for biomedical applications: future opportunity and challenges. NANOSCALE 2021; 13:16405-16426. [PMID: 34586121 DOI: 10.1039/d1nr04964j] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanotechnology is the most promising technology to evolve in the last decade. Recent research has shown that transition metal nanoparticles especially manganese (Mn)-based nanoparticles have great potential for various biomedical applications due to their unique fundamental properties. Therefore, globally, scientists are concentrating on the development of various new manganese-based nanoparticles (size and shape dependent) due to their indispensable utilities. Although numerous reports are available regarding the use of manganese nanoparticles, there is no comprehensive review highlighting the recent development of manganese-based nanomaterials and their potential applications in the area of biomedical sciences. The present review article provides an overall survey on the recent advancement of manganese nanomaterials in biomedical nanotechnology and other fields. Further, the future perspectives and challenges are also discussed to explore the wider application of manganese nanoparticles in the near future. Overall, this review presents a fundamental understanding and the role of manganese in various fields, which will attract a wider spectrum of the scientific community.
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Affiliation(s)
- Shagufta Haque
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad - 500007, Telangana State, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U.P., India
| | - Sanchita Tripathy
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad - 500007, Telangana State, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U.P., India
| | - Chitta Ranjan Patra
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad - 500007, Telangana State, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U.P., India
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Muntean CM, Ştefan R, Tǎbǎran A, Tripon C, Bende A, Fǎlǎmaş A, Colobǎţiu LM, Olar LE. The Influence of UV Femtosecond Laser Pulses on Bacterial DNA Structure, as Proved by Fourier Transform Infrared (FT‐IR) Spectroscopy. ChemistrySelect 2021. [DOI: 10.1002/slct.202102097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Cristina M. Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Rǎzvan Ştefan
- University of Agricultural Sciences and Veterinary Medicine Faculty of Veterinary Medicine 3–5 Calea Manastur Str. 400372 Cluj-Napoca Romania
| | - Alexandra Tǎbǎran
- University of Agricultural Sciences and Veterinary Medicine Faculty of Veterinary Medicine 3–5 Calea Manastur Str. 400372 Cluj-Napoca Romania
| | - Carmen Tripon
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Attila Bende
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Alexandra Fǎlǎmaş
- National Institute for Research & Development of Isotopic and Molecular Technologies 67-103 Donat Str. 400293 Cluj-Napoca Romania
| | - Liora M. Colobǎţiu
- Iuliu Haţieganu University of Medicine and Pharmacy Faculty of Pharmacy 8 Victor Babeş Str. 400012 Cluj-Napoca Romania
| | - Loredana E. Olar
- University of Agricultural Sciences and Veterinary Medicine Faculty of Veterinary Medicine 3–5 Calea Manastur Str. 400372 Cluj-Napoca Romania
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Siddiqui SS, Dhar C, Sundaramurthy V, Sasmal A, Yu H, Bandala-Sanchez E, Li M, Zhang X, Chen X, Harrison LC, Xu D, Varki A. Sialoglycan recognition is a common connection linking acidosis, zinc, and HMGB1 in sepsis. Proc Natl Acad Sci U S A 2021; 118:e2018090118. [PMID: 33658363 PMCID: PMC7958265 DOI: 10.1073/pnas.2018090118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Blood pH is tightly maintained between 7.35 and 7.45, and acidosis (pH <7.3) indicates poor prognosis in sepsis, wherein lactic acid from anoxic tissues overwhelms the buffering capacity of blood. Poor sepsis prognosis is also associated with low zinc levels and the release of High mobility group box 1 (HMGB1) from activated and/or necrotic cells. HMGB1 added to whole blood at physiological pH did not bind leukocyte receptors, but lowering pH with lactic acid to mimic sepsis conditions allowed binding, implying the presence of natural inhibitor(s) preventing binding at normal pH. Testing micromolar concentrations of divalent cations showed that zinc supported the robust binding of sialylated glycoproteins with HMGB1. Further characterizing HMGB1 as a sialic acid-binding lectin, we found that optimal binding takes place at normal blood pH and is markedly reduced when pH is adjusted with lactic acid to levels found in sepsis. Glycan array studies confirmed the binding of HMGB1 to sialylated glycan sequences typically found on plasma glycoproteins, with binding again being dependent on zinc and normal blood pH. Thus, HMGB1-mediated hyperactivation of innate immunity in sepsis requires acidosis, and micromolar zinc concentrations are protective. We suggest that the potent inflammatory effects of HMGB1 are kept in check via sequestration by plasma sialoglycoproteins at physiological pH and triggered when pH and zinc levels fall in late stages of sepsis. Current clinical trials independently studying zinc supplementation, HMGB1 inhibition, or pH normalization may be more successful if these approaches are combined and perhaps supplemented by infusions of heavily sialylated molecules.
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Affiliation(s)
- Shoib S Siddiqui
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093
| | - Chirag Dhar
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093
| | - Venkatasubramaniam Sundaramurthy
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093
| | - Aniruddha Sasmal
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093
| | - Hai Yu
- Department of Chemistry, University of California, Davis, CA 95616
| | - Esther Bandala-Sanchez
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Miaomiao Li
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14214
| | - Xiaoxiao Zhang
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14214
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA 95616
| | - Leonard C Harrison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ding Xu
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14214
| | - Ajit Varki
- Department of Medicine, University of California San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093
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Sabbatini M, Magnelli V, Renò F. NETosis in Wound Healing: When Enough Is Enough. Cells 2021; 10:cells10030494. [PMID: 33668924 PMCID: PMC7996535 DOI: 10.3390/cells10030494] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/15/2022] Open
Abstract
The neutrophils extracellular traps (NETs) are a meshwork of chromatin, histonic and non-histonic proteins, and microbicidal agents spread outside the cell by a series of nuclear and cytoplasmic events, collectively called NETosis. NETosis, initially only considered a defensive/apoptotic mechanism, is now considered an extreme defensive solution, which in particular situations induces strong negative effects on tissue physiology, causing or exacerbating pathologies as recently shown in NETs-mediated organ damage in COVID-19 patients. The positive effects of NETs on wound healing have been linked to their antimicrobial activity, while the negative effects appear to be more common in a plethora of pathological conditions (such as diabetes) and linked to a NETosis upregulation. Recent evidence suggests there are other positive physiological NETs effects on wound healing that are worthy of a broader research effort.
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Affiliation(s)
- Maurizio Sabbatini
- Department of Science and Innovation Technology (DISIT), Università del Piemonte Orientale—via T. Michel 11, 15121 Alessandria, Italy; (M.S.); (V.M.)
| | - Valeria Magnelli
- Department of Science and Innovation Technology (DISIT), Università del Piemonte Orientale—via T. Michel 11, 15121 Alessandria, Italy; (M.S.); (V.M.)
| | - Filippo Renò
- Innovative Research Laboratory for Wound Healing, Health Sciences Department, Università del Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
- Correspondence: ; Tel.: +39-0321-66-0634
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Muntean CM, Dina NE, Tǎbǎran A, Gherman AMR, Fǎlǎmaş A, Olar LE, Colobǎţiu LM, Ştefan R. Identification of Salmonella Serovars before and after Ultraviolet Light Irradiation by Fourier Transform Infrared (FT-IR) Spectroscopy and Chemometrics. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1731524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Cristina M. Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Nicoleta E. Dina
- National Institute for Research & Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Alexandra Tǎbǎran
- Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Ana M. R. Gherman
- National Institute for Research & Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Alexandra Fǎlǎmaş
- National Institute for Research & Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Loredana E. Olar
- Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Liora M. Colobǎţiu
- Faculty of Pharmacy, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Rǎzvan Ştefan
- Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
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Babić SD, Serec K. Sodium and manganese salt DNA thin films: An infrared spectroscopy study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 241:118646. [PMID: 32623301 DOI: 10.1016/j.saa.2020.118646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
In this work we have investigated influence of divalent Mn ions on the structure of dsDNA utilizing Fourier transform infrared spectroscopy on DNA thin films obtained from sodium and manganese salt DNA (Na-DNA and Mn-DNA) in manganese chloride solutions and manganese salt DNA in pure water. In the range of low Mn content, 0.0067 ≤ r = [manganese]/[phosphate] ≤ 0.5, the difference between vibrational spectrum of thin films Na-DNA and Mn-DNA is revealed. Former one is more influenced by an increase of Mn content and shows stabilization of B form dsDNA, while in thin films Mn-DNA in MnCl2 and Mn-DNA in pure water, B form is stable even at the lowest Mn content. An increase of Mn content over r > 0.5 induces spectral changes in both base and phosphate region that fully actualize once intrinsic Na+ ions are completely suppressed by divalent Mn2+ ions. Finally, the difference in vibrational spectrum of Na-DNA and Mn-DNA at high Mn concentrations almost completely disappears. The observed results consistently demonstrate that Mn2+ ions interact with both base sites of DNA (primarily C8N7 sites of guanine and adenine) and phosphate groups; both asymmetric and symmetric PO2 vibrations show prominent blue shift in the presence of high Mn content, while B conformation remains stable. Nature of the Mn cation-DNA interaction seems to be electrostatic and water mediated, as demonstrated by almost complete reversal of perturbations in base and sugar-phosphate region in thin films Mn-DNA in pure water.
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Affiliation(s)
- Sanja Dolanski Babić
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Kristina Serec
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; Centre of Excellence in Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, 10000 Zagreb, Croatia.
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Paston SV, Polyanichko AM, Shulenina OV, Osinnikova DN. A Study of the DNA Structure in Films Using FTIR Spectroscopy. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920060159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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15
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Telnaya EA, Plotnikova LV, Garifullin AD, Kuvshinov AY, Voloshin SV, Polyanichko AM. Infrared Spectroscopy of Blood Serum from Patients with Oncohematological Diseases. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920060214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Liu YF, Ran SY. Divalent metal ions and intermolecular interactions facilitate DNA network formation. Colloids Surf B Biointerfaces 2020; 194:111117. [PMID: 32512310 DOI: 10.1016/j.colsurfb.2020.111117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
Abstract
The interactions between divalent metal ions and DNA are crucial for basic life processes. These interactions are also important in advanced technological products such as DNA-based ion sensors. Current polyelectrolyte theories cannot describe these interactions well and do not consider the corresponding dynamics. In this study, we report the single-molecule dynamics of the binding of divalent metal ions to a single DNA molecule and the morphology characterization of the complex. We found that most of the divalent metal ions (Mn2+, Zn2+, Co2+, Ni2+, and Cd2+), except Mg2+ and Ca2+, could cause monomolecular DNA condensation. For transition metal ions, different ionic strengths were required to induce the compaction, and different shortening speeds were displayed in the dynamics, indicating ionic specificity. Atomic force microscopy revealed that the morphologies of the metal ion-DNA complexes were affected by the ionic strength of the metal ion, DNA chain length, and DNA concentration. At low metal ion concentration, DNA tended to adopt a random coil conformation. Increasing the ionic strength led to network-like condensed structures, suggesting that divalent metal ions can induce attraction between DNA molecules. Furthermore, higher DNA concentration and longer chain length enhanced intermolecular interactions and consequently resulted in network structures with a higher degree of interconnectivity.
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Affiliation(s)
- Yin-Feng Liu
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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17
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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18
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Kiran T, Pathak M, Chanda K, Balamurali MM. DNA and Protein Interaction Studies of Heteroleptic Copper (II) Derivatives of Benzothiazole‐Based Schiff Base and N,N‐Donor Ligands. ChemistrySelect 2020. [DOI: 10.1002/slct.202001246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tummalapalli Kiran
- Department of ChemistryScience and HumanitiesJ. B. Institute of Engineering and Technology Moinabad Hyderabad 500075 India
| | - Madhvesh Pathak
- Department of ChemistrySchool of Advanced SciencesVellore Institute of Technology Vellore 632014 Tamilnadu India
| | - Kaushik Chanda
- Department of ChemistrySchool of Advanced SciencesVellore Institute of Technology Vellore 632014 Tamilnadu India
| | - M. M. Balamurali
- Chemistry DivisionSchool of Advanced SciencesVellore Institute of Technology Chennai Campus Chennai 600127 Tamilnadu India
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19
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Savchenkov A, Demina L, Safonov A, Grigoriev M, Solovov R, Abkhalimov E. Syntheses and crystal structures of new aurate salts of adenine or guanine nucleobases. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:139-147. [PMID: 32022708 DOI: 10.1107/s2053229619016656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/11/2019] [Indexed: 11/10/2022]
Abstract
Two new gold(III) complexes with adenine or guanine nitrogenous bases as counter-cations were synthesized. These are 6-amino-7H-purine-1,9-diium tetrachloridogold(III) chloride monohydrate, (C5H7N5)[AuCl4]Cl·H2O, 1, and 2-amino-6-oxo-6,7-dihydro-1H-purin-9-ium tetrachloridogold(III) hemihydrate, (C5H6N5O)[AuCl4]·0.5H2O, 2. Their crystal structures were studied using single-crystal X-ray diffraction and FT-IR spectroscopic techniques. The arrangement of species in the studied crystal structures implies π-stacking interactions, as well as concomitant C-H...π interactions, hydrogen bonds and other types of noncovalent interactions, which were studied qualitatively and quantitatively using the method of molecular Voronoi-Dirichlet polyhedra. The variation of the nitrogenous base from adenine to guanine results in evident differences in the packing of the species in the crystals of 1 and 2. The splitting and shifting of bands in the FT-IR spectra of the title compounds reveals several features representative of noncovalent interactions in their crystal structures.
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Affiliation(s)
- Anton Savchenkov
- Samara National Research University, Samara 443011, Russian Federation
| | - Ludmila Demina
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Science, Leninskii pr. 31-4, Moscow 119071, Russian Federation
| | - Alexey Safonov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Science, Leninskii pr. 31-4, Moscow 119071, Russian Federation
| | - Mikhail Grigoriev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Science, Leninskii pr. 31-4, Moscow 119071, Russian Federation
| | - Roman Solovov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Science, Leninskii pr. 31-4, Moscow 119071, Russian Federation
| | - Evgeny Abkhalimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Science, Leninskii pr. 31-4, Moscow 119071, Russian Federation
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20
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Takahashi S, Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 2020; 49:8439-8468. [DOI: 10.1039/d0cs00594k] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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21
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Adegoke OA, Ghosh M, Jana A, Mukherjee A. Photo-physical investigation of the binding interactions of alumina nanoparticles with calf thymus DNA. THE NUCLEUS 2019. [DOI: 10.1007/s13237-019-00301-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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22
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Kumar M, Kumar G, Mogha NK, Jain R, Hussain F, Masram DT. Structure, DNA/proteins binding, docking and cytotoxicity studies of copper(II) complexes with the first quinolone drug nalidixic acid and 2,2'‑dipyridylamine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 212:94-104. [PMID: 30616168 DOI: 10.1016/j.saa.2018.12.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/18/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
This work presents the synthesis, structural characterization and biological affinity of the newly synthesized copper(II) complexes with the first antibacterial quinolone drug nalidixic acid (nal) or N-donor ligand 2,2'‑dipyridylamine (bipyam). [Cu(II)(nal)(bipyam)Cl], (2) reveals a distorted square pyramidal based geometry in Cu(II) atom confirmed by X-ray crystallography technique. The theoretical stabilities and optimized structures of the complex were obtained from DFT calculations. The ability of the complexes to bind with calf thymus DNA (CT DNA) were investigated by electronic absorption, fluorescence, circular dichroism, and viscosity measurements techniques. The experimental results reveal that the complexes strongly interact with CT DNA via intercalative mode but complex 2 exhibits the highest affinity giving Kb=3.91±0.13×106, M-1. The fluorescence spectroscopy measurements show that both complexes have the superior ability to the replacement of EtBr from DNA-bound EtBr solution and bind to DNA through intercalative mode. Both complex also shows the superior affinity towards proteins with comparatively high binding constant values which have been further revealed by fluorescence spectroscopy measurements. Molecular docking analysis indicates that the interaction of the complexes and proteins are stabilized by hydrogen bonding and hydrophobic interaction. Furthermore, the results of in vitro cytotoxicity reveal that the complex 2 has excellent cytotoxicity than 1 against human breast cancer cell lines (MCF-7).
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Affiliation(s)
- Manish Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Gyanendra Kumar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | | | - Ritu Jain
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Firasat Hussain
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Dhanraj T Masram
- Department of Chemistry, University of Delhi, Delhi 110007, India.
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23
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Sedighipoor M, Kianfar AH, Mohammadnezhad G, Görls H, Plass W, Momtazi-Borojeni AA, Abdollahi E. Synthesis, crystal structure of novel unsymmetrical heterocyclic Schiff base Ni(II)/V(IV) complexes: Investigation of DNA binding, protein binding and in vitro cytotoxic activity. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.12.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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24
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Movahedi E, Rezvani AR, Razmazma H. Binding interaction of a heteroleptic silver(I) complex with DNA: A joint experimental and computational study. Int J Biol Macromol 2019; 126:1244-1254. [PMID: 30615962 DOI: 10.1016/j.ijbiomac.2019.01.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
Abstract
A new heteroleptic Ag(I) complex formulated as [Ag(daf)(phen)]NO3, where daf and phen stand for 4,5-diazafluoren-9-one and 1,10-phenanthroline, respectively, has been prepared and structurally characterized by elemental analysis, spectroscopic methods (IR, 1HNMR, and UV-Vis) and cyclic voltammetry. The geometry optimization around Ag(I) at the level of DFT has demonstrated that the Ag(I) center has been nested in a tetrahedral N4 coordination geometry which found to be in close agreement with the experimentally proposed structure. The bond lengths, angles, and the HOMO/LUMO energies have been calculated to substantiate the geometry of the complex. The DNA binding property of the Ag(I) complex has been explored in detail both theoretically (DFT and molecular docking) and experimentally (UV-Vis absorption spectroscopy, circular dichroism spectroscopy, luminescence quenching, competitive binding with ethidium bromide, cyclic voltammetry, and gel electrophoresis), indicating the good affinity of the Ag(I) complex for the intercalation (Kb (binding constant) = 3.45 × 105 M-1). Providing a fuller picture of Ag(I) complex-DNA interaction, the energy-minimized structure of the complex has been docked to the DNA with a d(AGACGTCT)2 sequence and the results are in close agreement with experimental achievements and make a deeper insight into the relationship between the structure and biological activity of the complex.
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Affiliation(s)
- Elaheh Movahedi
- Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan, Iran
| | - Ali Reza Rezvani
- Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan, Iran.
| | - Hafez Razmazma
- Department of Chemistry, Laboratory of Computational Quantum Chemistry and Drug Design, University of Sistan and Baluchestan, Zahedan, Iran
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25
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Kumar M, Masram DT. Evaluation of DNA, BSA, and HSA binding propensity of copper(II) complex with N-donor ligand 2,2′-dipyridylamine. Polyhedron 2019. [DOI: 10.1016/j.poly.2018.10.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Kanellis VG, Dos Remedios CG. A review of heavy metal cation binding to deoxyribonucleic acids for the creation of chemical sensors. Biophys Rev 2018; 10:1401-1414. [PMID: 30229467 DOI: 10.1007/s12551-018-0455-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022] Open
Abstract
Various human activities lead to the pollution of ground, drinking, and wastewater with toxic metals. It is well known that metal ions preferentially bind to DNA phosphate backbones or DNA nucleobases, or both. Foreman et al. (Environ Toxicol Chem 30(8):1810-1818, 2011) reported the use of a DNA-dye based assay suitable for use as a toxicity test for potable environmental water. They compared the results of this test with the responses of live-organism bioassays. The DNA-based demonstrated that the loss of SYBR Green I fluorescence dye bound to calf thymus DNA was proportional to the toxicity of the water sample. However, this report raised questions about the mechanism that formed the basis of this quasi-quantitatively test. In this review, we identify the unique and preferred DNA-binding sites of individual metals. We show how highly sensitive and selective DNA-based sensors can be designed that contain multiple binding sites for 21 heavy metal cations that bind to DNA and change its structure, consistent with the release of the DNA-bound dye.
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27
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Zhou Y, Song T, Cao Y, Gong G, Zhang Y, Zhao H, Zhao G. Synthesis and characterization of planar chiral cyclopalladated ferrocenylimines: DNA/HSA interactions and in vitro cytotoxic activity. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.06.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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28
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Das S, Mukhopadhyay S, Chatterjee S, Devi PS, Suresh Kumar G. Fluorescent ZnO-Au Nanocomposite as a Probe for Elucidating Specificity in DNA Interaction. ACS OMEGA 2018; 3:7494-7507. [PMID: 30087915 PMCID: PMC6068853 DOI: 10.1021/acsomega.7b02096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/08/2018] [Indexed: 05/10/2023]
Abstract
In this work, we report the interaction of a fluorescent ZnO-Au nanocomposite with deoxyribonucleic acid (DNA), leading to AT-specific DNA interaction, which is hitherto not known. For this study, three natural double-stranded (ds) DNAs having different AT:GC compositions were chosen and a ZnO-Au nanocomposite has been synthesized by anchoring a glutathione-protected gold nanocluster on the surface of egg-shell-membrane (ESM)-based ZnO nanoparticles. The ESM-based bare ZnO nanoparticles did not show any selective interaction toward DNA, whereas intrinsic fluorescence of the ZnO-Au nanocomposite shows an appreciable blue shift (Δλmax = 18 nm) in the luminescence wavelength of 520 nm in the presence of ds calf thymus (CT) DNA over other studied DNAs. In addition, the interaction of the nanocomposite through fluorescence studies with single-stranded (ss) CT DNA, synthetic polynucleotides, and nucleobases/nucleotides (adenine, thymine, deoxythymidine monophosphate, deoxyadenosine monophosphate) was also undertaken to delineate the specificity in interaction. A minor blue shift (Δλmax = 5 nm) in the emission wavelength at 520 nm was observed for single-stranded CT DNA, suggesting the proficiency of the nanocomposite for discriminating ss and ds CT DNA. More importantly, fluorescence signals from the nano-bio-interaction could be measured directly without any modification of the target, which is the foremost advantage emanated from this study compared with other previous reports. The AT base-pair-induced enhancement was also found to be highest for the melting temperature of CT DNA (ΔTmCT = 6.7 °C). Furthermore, spectropolarimetric experiments followed by calorimetric analysis provided evidence for specificity in AT-rich DNA interaction. This study would lead to establish the fluorescent ZnO-Au nanocomposite as a probe for nanomaterial-based DNA-binding study, featuring its specific interaction toward AT-rich DNA.
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Affiliation(s)
- Sumita Das
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
| | - Soumita Mukhopadhyay
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
| | - Sabyasachi Chatterjee
- Biophysical
Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Parukuttyamma Sujatha Devi
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
- E-mail: , . Phone: +91-33-2483
8082. Fax: 91-33-2473 0957
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
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29
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Sedighipoor M, Kianfar AH, Sabzalian MR, Abyar F. Synthesis and characterization of new unsymmetrical Schiff base Zn (II) and Co (II) complexes and study of their interactions with bovin serum albumin and DNA by spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 198:38-50. [PMID: 29505940 DOI: 10.1016/j.saa.2018.02.050] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/06/2018] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Two novel tetra-coordinated Cobalt(II) and Zinc (II) chelate series with the general formula of [Co (L)·2H2O] (1) and [Zn (L)] (2) [L=N-2-hydroxyacetophenon-N'-2-hydroxynaphthaldehyde-1,2 phenylenediimine)] with biologically active Schiff base ligands were synthesized and recognized by elemental analysis and multi-nuclear spectroscopy (IR and 1H and 13C NMR); then, their biological activities including DNA and protein interactions were studied. The interaction of the synthesized compounds with bovine serum albumin (BSA) was investigated via fluorescence spectroscopy, showing the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary BSA structure in the presence of the complexes. The interaction of these compounds with CT-DNA was considered by UV-Vis technique, emission titration, viscosity measurements, helix melting methods, and circular dichroism (CD) spectroscopy, confirming that the complexes were bound to CT-DNA by the intercalation binding mode. Furthermore, the complexes had the capability to displace the DNA-bound MB, as shown by the competitive studies of these complexes with methylene blue (MB), thereby suggesting the intercalation mode for the competition. Finally, the theoretical studies carried out by the docking method were performed to calculate the binding constants and recognize the binding site of the BSA and DNA by the complexes. In addition, in vitro and in silico studies showed that the compounds were degradable by bacterial and fungal biodegradation activities.
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Affiliation(s)
- Maryam Sedighipoor
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Ali Hossein Kianfar
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran.
| | - Mohammad R Sabzalian
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Fatemeh Abyar
- Department of Chemical Engineering, Faculty of Engineering, Ardakan University, Ardakan 89518-95491, Iran
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30
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Multispectroscopic DNA-Binding studies and antimicrobial evaluation of new mixed-ligand Silver(I) complex and nanocomplex: A comparative study. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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31
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Hirbod S, Nafisi S, Maibach HI. RNA Loading on Nano-Structured Hyperbranched β-Cyclodextrin. Avicenna J Med Biotechnol 2018; 10:15-21. [PMID: 29296262 PMCID: PMC5742648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND β-Cyclodextrin functionalized hyper-branched polyglycerol (HBCD: β-CD-g-PG), a biocompatible polymer, has recently been proposed for delivery of poorly water soluble compounds. METHODS The present study examines the interaction of HBCD with RNA, utilizing a constant concentration of RNA and different HBCD/RNA ratios of 1/16 to 1/1, at physiological condition in an aqueous solution. Circular Dichroism (CD), UV-visible, FTIR spectroscopic methods, zeta potential and Dynamic Light Scattering (DLS) were used to analyze the particle formation, particle charge, particle size, aggregation, RNA conformation, binding constant and mode, and the effect of polymer complexation on RNA stability. RESULTS The results indicate that the interaction of RNA with HBCD leads to the formation of a linear dendritic supramolecule biopolymer with an overall binding constant of KHBCD/RNA= 1.25 × 103. CONCLUSION The small sized synthesized polymer can be considered as an appropriate system for preventing RNA aggregation and protecting the gene by host-guest interaction.
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Affiliation(s)
- Sorina Hirbod
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Shohreh Nafisi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran,Department of Dermatology, University of California, San Francisco, CA, USA,Corresponding authors: Shohreh Nafisi, Ph.D., Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Howard I Maibach
- Department of Dermatology, University of California, San Francisco, CA, USA,Howard I Maibach, Ph.D., Department of Dermatology, University of California, San Francisco, USA, Tel: +98 21 22426554, +1 415 7535304, E-mail: ,
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Asaadi S, Hajian R. DNA binding studies of Sunset Yellow FCF using spectroscopy, viscometry and electrochemical techniques. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.06.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Belaya I, Chikhirzhina E, Polyanichko A. Interaction of DDP with bovine serum albumin facilitates formation of the protein dimers. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Tabassum S, Afzal M, Al–Lohedan H, Zaki M, Khan RA, Ahmad M. Synthesis and structure elucidation of new open cubane tetranuclear [Cu II 4 ] Cluster: Evaluation of the DNA/HSA interaction and pBR322 DNA cleavage pathway and cytotoxicity. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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Characterization of tRNALeu binding interactions with Cu2+ and Pb2+ and their biological implications. J Inorg Biochem 2017; 171:90-99. [DOI: 10.1016/j.jinorgbio.2017.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/12/2017] [Accepted: 03/19/2017] [Indexed: 11/17/2022]
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36
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Paston SV, Polyanichko AM, Shulenina OV. Study of DNA interactions with Cu2+ and Mg2+ ions in the presence of caffeine. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617020263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sanchez OF, Lee J, Yu King Hing N, Kim SE, Freeman JL, Yuan C. Lead (Pb) exposure reduces global DNA methylation level by non-competitive inhibition and alteration of dnmt expression. Metallomics 2017; 9:149-160. [DOI: 10.1039/c6mt00198j] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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38
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Rane LB, Kate AN, Ramteke SN, Shravage BV, Kulkarni PP, Kumbhar AA. Fluorescent zinc(ii) complexes for gene delivery and simultaneous monitoring of protein expression. Dalton Trans 2016; 45:16984-16996. [PMID: 27711702 DOI: 10.1039/c6dt02871c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two new zinc(ii) complexes, [Zn(l-His)(NIP)]+(1) and [Zn(acac)2(NIP)](2) (where NIP is 2-(naphthalen-1-yl)-1H-imidazo[4,5-f][1,10]phenanthroline, acac = acetyl acetone), have been synthesized and characterized by elemental analysis, UV-vis, fluorescence, IR, 1H NMR and electron spray ionization mass spectroscopies. Gel retardation assay, atomic force microscopy and dynamic light scattering studies show that 1 and 2 can induce the condensation of circular plasmid pBR322 DNA into nanometer size particles under ambient conditions. Treatment of 2 with 5 mM EDTA restored 30% of the supercoiled form of DNA, revealing partial reversibility of DNA condensation. The in vitro transfection experiment demonstrates that the complexes can be used to deliver pCMV-tdTomato-N1 plasmid which expresses red fluorescent protein. The confocal studies show that the fluorescent nature of complexes is advantageous for visualizing the intracellular delivery of metal complexes as well as transfection efficiency using two distinct emission windows.
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Affiliation(s)
- Lalita B Rane
- Department of Chemistry, Savitribai Phule Pune University, Pune - 411007, India.
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Tummalapalli K, C S V, Munusami P, Pathak M, M M B. Evaluation of DNA/Protein interactions and cytotoxic studies of copper(II) complexes incorporated with N, N donor ligands and terpyridine ligand. Int J Biol Macromol 2016; 95:1254-1266. [PMID: 27838416 DOI: 10.1016/j.ijbiomac.2016.11.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 12/23/2022]
Abstract
A series of four new copper(II) heteroleptic complexes, [Cu(2‴-pytpy) (L)] (NO3)2·2H2O (1-4), where 2‴-pytpy=4'-(2'''-Pyridyl)-2, 2':6', 2''-terpyridine, L=bipyridyl (bpy), 1, 10 phenanthroline(phen), dipyridoquinoxaline(dpq) and dipyridophenazine (dppz) were synthesized and characterized by spectroscopic techniques. Further, the molecular structure of the complex (2) was confirmed by single crystal X-ray diffraction technique and the data revealed a penta coordinated, distorted square-pyramidal geometry with triclinic system. The interactions of four complexes with calf thymus DNA and bovine serum albumin (BSA) were investigated by electronic absorption, fluorescence and circular dichroism spectroscopy techniques. Spectral studies substantiated an intercalative binding mode of metal complexes with ct-DNA. Significant binding interactions of the complexes with protein have been further revealed from fluorescence studies. Furthermore, all the four complexes show potential cytotoxicity towards the human liver carcinoma cell line (HepG-2).
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Affiliation(s)
- Kiran Tummalapalli
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, Tamilnadu 632014, India
| | - Vasavi C S
- Bioinformatics Division, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu 632 014, India
| | - Punnagai Munusami
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Madhvesh Pathak
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, Tamilnadu 632014, India.
| | - Balamurali M M
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, Tamilnadu 632014, India.
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Serec K, Babić SD, Podgornik R, Tomić S. Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study. Nucleic Acids Res 2016; 44:8456-64. [PMID: 27484473 PMCID: PMC5041487 DOI: 10.1093/nar/gkw696] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/27/2016] [Indexed: 11/14/2022] Open
Abstract
Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift and the intensity of asymmetric PO2 stretching band decrease, indicating an increase of magnesium-phosphate binding in the backbone region. Vibration characteristics of the A conformation of the dsDNA vanish, whereas those characterizing the B conformation become fully stabilized. In the crossover range with comparable Mg and intrinsic Na DNA ions ([Mg]/[P] ≈ 1) B conformation remains stable; vibrational spectra show moderate intensity changes and a prominent blue shift, indicating a reinforcement of the bonds and binding in both the phosphate and the base regions. The obtained results reflect the modified screening and local charge neutralization of the dsDNA backbone charge, thus consistently demonstrating that the added Mg ions interact with DNA via long-range electrostatic forces. At high Mg contents ([Mg]/[P] > 10), the vibrational spectra broaden and show a striking intensity rise, while the base stacking remains unaffected. We argue that at these extreme conditions, where a charge compensation by vicinal counterions reaches 92-94%, DNA may undergo a structural transition into a more compact form.
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Affiliation(s)
- Kristina Serec
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - Sanja Dolanski Babić
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute, Ljubljana, 1000, Slovenia Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, 1000, Slovenia
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Thamilarasan V, Sengottuvelan N, Stalin N, Srinivasan P, Chakkaravarthi G. Synthesis, interactions, molecular structure, biological properties and molecular docking studies on Mn, Co, Zn complexes containing acetylacetone and pyridine ligands with DNA duplex. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 160:110-20. [DOI: 10.1016/j.jphotobiol.2016.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 02/20/2016] [Accepted: 03/14/2016] [Indexed: 12/24/2022]
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42
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Direct Evidence of Divalent Manganese Ion-Induced DNA Condensation at Room Temperature. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201600123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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Synthesis, characterization, cytotoxic activity and DNA-binding studies of cobalt (II) mixed-ligand complex containing pyridine-2,6-dicarboxylate ion and 2-aminopyrimidine. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2016. [DOI: 10.1007/s13738-016-0826-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Mahendiran D, Kumar RS, Viswanathan V, Velmurugan D, Rahiman AK. Targeting of DNA molecules, BSA/c-Met tyrosine kinase receptors and anti-proliferative activity of bis(terpyridine)copper(ii) complexes. Dalton Trans 2016; 45:7794-814. [DOI: 10.1039/c5dt03831f] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The newly synthesized bis(terpyridine)copper(ii) complexes may act as DNA-targeting metallo-anticancer agents to overcome cisplatin resistance.
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Affiliation(s)
- Dharmasivam Mahendiran
- Post-Graduate and Research Department of Chemistry
- The New College (Autonomous)
- Chennai 600 014
- India
| | - Raju Senthil Kumar
- Department of Pharmaceutical Chemistry
- Swami Vivekanandha College of Pharmacy
- Tiruchengodu 637 205
- India
| | - Vijayan Viswanathan
- CAS in Crystallography and Biophysics
- University of Madras
- Guindy Campus
- Chennai 600 025
- India
| | - Devadasan Velmurugan
- CAS in Crystallography and Biophysics
- University of Madras
- Guindy Campus
- Chennai 600 025
- India
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry
- The New College (Autonomous)
- Chennai 600 014
- India
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46
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Abassi Joozdani F, Yari F, Abassi Joozdani P, Nafisi S. Interaction of sulforaphane with DNA and RNA. PLoS One 2015; 10:e0127541. [PMID: 26030290 PMCID: PMC4452540 DOI: 10.1371/journal.pone.0127541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/16/2015] [Indexed: 01/19/2023] Open
Abstract
Sulforaphane (SFN) is an isothiocyanate found in cruciferous vegetables with anti-inflammatory, anti-oxidant and anti-cancer activities. However, the antioxidant and anticancer mechanism of sulforaphane is not well understood. In the present research, we reported binding modes, binding constants and stability of SFN-DNA and -RNA complexes by Fourier transform infrared (FTIR) and UV-Visible spectroscopic methods. Spectroscopic evidence showed DNA intercalation with some degree of groove binding. SFN binds minor and major grooves of DNA and backbone phosphate (PO2), while RNA binding is through G, U, A bases with some degree of SFN-phosphate (PO2) interaction. Overall binding constants were estimated to be K(SFN-DNA)=3.01 (± 0.035)×10(4) M(-1) and K(SFN-RNA)= 6.63 (±0.042)×10(3) M(-1). At high SFN concentration (SFN/RNA = 1/1), DNA conformation changed from B to A occurred, while RNA remained in A-family structure.
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Affiliation(s)
| | - Faramarz Yari
- Department of Biology, IAU, Science and Research Branch, Tehran, Iran
| | | | - Shohreh Nafisi
- Department of Chemistry, IAU, Central Tehran Branch, Tehran, Iran
- Department of Dermatology, University of California, San Francisco, California, United States of America
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Karami K, Lighvan ZM, Barzani SA, Faal AY, Poshteh-Shirani M, Khayamian T, Eigner V, Dušek M. Design and synthesis of a novel trinuclear palladium(ii) complex containing an oxime chelate ligand: determining the interaction mechanism with the DNA groove and BSA site I by spectroscopic and molecular dynamics simulation approaches. NEW J CHEM 2015. [DOI: 10.1039/c5nj01280e] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The trinuclear Pd(II) complex containing an oxime ligand showed significant interaction with both CT-DNA and BSA.
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Affiliation(s)
- Kazem Karami
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- Iran
| | | | | | - Ali Yeganeh Faal
- Department of Chemistry
- Faculty of Science
- Payam Noor University
- Iran
| | | | - Taghi Khayamian
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- Iran
| | | | - Michal Dušek
- Institute of Physics AS CR
- Prague 8
- Czech Republic
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UV degradation of genomic DNA from in vitro grown plant species: A Fourier transform infrared spectroscopic assessment. Polym Degrad Stab 2014. [DOI: 10.1016/j.polymdegradstab.2014.05.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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50
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Rajalakshmi S, Kiran MS, Nair BU. DNA condensation by copper(II) complexes and their anti-proliferative effect on cancerous and normal fibroblast cells. Eur J Med Chem 2014; 80:393-406. [DOI: 10.1016/j.ejmech.2014.04.064] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/17/2014] [Accepted: 04/22/2014] [Indexed: 12/18/2022]
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