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Xiang H, Valandro SR, Hill EH. Layered silicate edge-linked perylene diimides: Synthesis, self-assembly and energy transfer. J Colloid Interface Sci 2023; 629:300-306. [PMID: 36155925 DOI: 10.1016/j.jcis.2022.09.055] [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: 05/26/2022] [Revised: 09/02/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022]
Abstract
The control over intermolecular interactions between chromophores at nanomaterial interfaces is important for sensing and light-harvesting applications. To that aim, inorganic nanoparticles with anisotropic shape and surface chemistry can serve as useful supports for organic modification. Herein, novel asymmetric perylene diimides with aspartic acid and oleyl terminal groups were grafted to the edges of the layered silicate clay Laponite, a water-dispersible discoidal nanoparticle. The photophysical properties and solvent-dependent self-assembly of the nanoclay-grafted perylenes were investigated, revealing that the polarity of the terminating ligand dictates the aggregation behavior in aqueous solution, where increased water content generally led to the formation of perylene H-aggregates. The anionic basal surface of the nanoclay provided a binding site for a cationic fluorophore, leading to energy transfer from the face-bound donor to the edge-bound perylene acceptor. This study encourages further research on the use of functional ligands for the formation of organic-inorganic hybrids, particularly where inorganic template particles with specific surface chemistry can be exploited to study intermolecular interactions. Overall, these findings should advance further design and implementation of novel semiconducting ligands towards inorganic-organic hybrids, with potential applications in sensing and energy harvesting.
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Affiliation(s)
- Hongxiao Xiang
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Silvano R Valandro
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; The Hamburg Center for Ultrafast Imaging (CUI), Luruper Chausee 149, 22761 Hamburg, Germany
| | - Eric H Hill
- Institute of Physical Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany; The Hamburg Center for Ultrafast Imaging (CUI), Luruper Chausee 149, 22761 Hamburg, Germany.
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2
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Bisoi A, Sarkar S, Chandra Singh P. Contrasting Effect of Salts on the Binding of Antimalarial Drug Hydroxychloroquine with Different Sequences of Duplex DNA. J Phys Chem B 2022; 126:5605-5612. [PMID: 35867068 DOI: 10.1021/acs.jpcb.2c02755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxychloroquine (HCQ) is an important antimalarial drug which functions plausibly by targeting the DNA of parasites. Salts play a crucial role in the functionality of various biological processes. Hence, the effect of salts (NaCl and MgCl2) on the binding of HCQ with AT- and CG-DNAs as well as the binding-induced stability of both sequences of DNAs have been investigated using the spectroscopic and molecular dynamics (MD) simulation methods. It has been found that the effect of salts on the binding of HCQ is highly sensitive to the nature of ions as well as DNA sequences. The effect of ions is opposite for the binding of AT- and CG-DNAs as the presence of Mg2+ ions enhances the binding of HCQ with AT-DNA, whereas the binding of HCQ with CG-DNA gets decreased on the addition of both ions. Similarly, the presence of Mg2+ enhances the stabilization of HCQ-bound AT-DNA, whereas the effect is opposite for the CG-DNA in the presence of both the ions. The MD simulation study suggests that the hydration states of both ions are different and they interact differently in the minor and major grooves of both the sequences of DNA which may be one of the reasons for the different binding of HCQ with these two sequences of DNA in the presence of salts. The information about the effect of salts on the binding of HCQ with DNAs in a sequence-specific manner may be useful in understanding the mechanism of the action and toxicity effect of HCQ against malaria.
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Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Mir SA, Dash GC, Meher RK, Mohanta PP, Chopdar KS, Mohapatra PK, Baitharu I, Behera AK, Raval MK, Nayak B. In Silico and In Vitro Evaluations of Fluorophoric Thiazolo-[2,3-b]quinazolinones as Anti-cancer Agents Targeting EGFR-TKD. Appl Biochem Biotechnol 2022; 194:4292-4318. [PMID: 35366187 DOI: 10.1007/s12010-022-03893-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/14/2022] [Indexed: 12/01/2022]
Abstract
Epidermal growth factor receptor tyrosine kinase domain (EGFR-TKD) plays a pivotal role in cellular signaling, growth, and metabolism. The EGFR-TKD is highly expressed in cancer cells and was endorsed as a therapeutic target for cancer management to overcome metastasis, cell proliferation, and angiogenesis. The novel thiazolo-[2,3-b]quinazolinones series were strategically developed by microwave-assisted organic synthesis and multi dominos reactions aimed to identify the potent thiazolo-[2,3-b]quinazolinone inhibitor against EGFR-TKD. This study explores the binding stability and binding strength of newly developed series via molecular docking, molecular dynamics simulation, and MM/PBSA and MM/GBSA calculations. The binding interaction was observed to be through the functional groups on aryl substituents at positions 3 and 5 of the thiazolo-[2, 3-b]quinazolinone scaffold. The methyl substituents at position 8 of the ligands had prominent hydrophobic interactions corroborating their bindings similar to the reference FDA-approved drug erlotinib in the active site. ADMET predictions reveal that derivatives 5ab, 5aq, and 5bq are drug-like and may be effective in in vitro study. Molecular dynamics simulation for 100 ns of docked complexes revealed their stability at the atomistic level. The ΔGbinding of thiazolo-[2,3-b]quinazolinone was found to be 5ab - 22.45, 5aq - 22.23, and 5bq - 20.76 similar to standard drug, and erlotinib - 24.11 kcal/mol was determined by MM/GBSA method. Furthermore, the anti-proliferative activity of leads of thiazolo-[2,3-b]quinazolinones (n = 3) was studied against breast cancer cell line (MCF-7) and non-small lung carcinoma cell line (H-1299). The highest inhibitions in cell proliferation were shown by 5bq derivatives, and the IC50 was found to be 6.5 ± 0.67 µM against MCF-7 and 14.8 µM against H-1299. The noscapine was also taken as a positive control and showed IC50 at higher concentrations 37 ± 1 against MCF-7 and 46.5 ± 1.2 against H-1299.
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Affiliation(s)
- Showkat Ahmad Mir
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | | | - Rajesh Kumar Meher
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | | | | | - Pranab Kishor Mohapatra
- Department of Chemistry, C. V. Raman Global University, Bidyanagar, Mahura, Janla, Bhubaneswar, Odisha, 752054, India.
| | - Iswar Baitharu
- Department of Environmental Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | - Ajaya Kumar Behera
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, 768019, India
| | - Mukesh Kumar Raval
- School of Chemistry, Gangadhar Meher University, Sambalpur, Odisha, 768004, India.
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, 768019, India.
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Interactions between a dsDNA Oligonucleotide and Imidazolium Chloride Ionic Liquids: Effect of Alkyl Chain Length, Part I. Molecules 2021; 27:molecules27010116. [PMID: 35011348 PMCID: PMC8746396 DOI: 10.3390/molecules27010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/23/2022] Open
Abstract
Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium chloride ([Imn,1]+) ionic liquids and a synthetic DNA oligonucleotide composed entirely of T/A bases (7(TA)) to elucidate the effects ILs on a model DNA duplex. Spectral shifts on the order of 500–1000 cm−1, spectral broadening (~1000 cm−1), and excitation and emission intensity ratio changes combine to give evidence of an increased DAPI environment heterogeneity on added IL. Fluorescence lifetimes for DAPI/IL solutions yielded two time constants 0.15 ns (~80% to 60% contribution) and 2.36–2.71 ns for IL up to 250 mM. With DNA, three time constants were required that varied with added IL (0.33–0.15 ns (1–58% contribution), ~1.7–1.0 ns (~5% contribution), and 3.8–3.6 ns (94–39% contribution)). MD radial distribution functions revealed that π-π stacking interactions between the imidazolium ring were dominant at lower IL concentration and that electrostatic and hydrophobic interactions become more prominent as IL concentration increased. Alkyl chain alignment with DNA and IL-IL interactions also varied with IL. Collectively, our data showed that, at low IL concentration, IL was primarily bound to the DNA minor groove and with increased IL concentration the phosphate regions and major groove binding sites were also important contributors to the complete set of IL-DNA duplex interactions.
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DNA Dyes-Highly Sensitive Reporters of Cell Quantification: Comparison with Other Cell Quantification Methods. Molecules 2021; 26:molecules26185515. [PMID: 34576986 PMCID: PMC8465179 DOI: 10.3390/molecules26185515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Cell quantification is widely used both in basic and applied research. A typical example of its use is drug discovery research. Presently, plenty of methods for cell quantification are available. In this review, the basic techniques used for cell quantification, with a special emphasis on techniques based on fluorescent DNA dyes, are described. The main aim of this review is to guide readers through the possibilities of cell quantification with various methods and to show the strengths and weaknesses of these methods, especially with respect to their sensitivity, accuracy, and length. As these methods are frequently accompanied by an analysis of cell proliferation and cell viability, some of these approaches are also described.
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Sarkar S, Roy S, Singh PC. Groove Switching of Hydroxychloroquine Modulates the Efficacy of Binding and Induced Stability to DNA. J Phys Chem B 2021; 125:6889-6896. [PMID: 34137627 DOI: 10.1021/acs.jpcb.1c03869] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxychloroquine (HCQ) is an important drug for the treatment of rheumatoid arthritis and malaria. HCQ targets specifically to nucleic acids for its action. However, the mechanism of HCQ binding and the effect of its binding on the stability of DNA are elusive. In this study, the binding mechanism of HCQ and the effect of binding on stability of different sequences of DNA have been investigated using spectroscopic and molecular dynamics (MD) simulation techniques. HCQ binds with all of the sequences of DNA and stabilizes them. However, binding efficacy of HCQ with DNA depends on its sequences as the binding constant is highest for pure guanine-cytosine (G-C) rich DNA and decreases with the increase of adenine-thymine (A-T) bases. HCQ prefers to interact with AT DNA through the minor groove whereas the major groove along with intercalation are the favorable binding mode in the case of GC DNA. The binding of HCQ in the major groove of GC DNA enhances the stacking between the bases compared to the case of AT DNA which leads to higher stability for GC DNA. It appears that the groove switching of HCQ is correlated with binding affinity as well as stability of different sequences of DNA.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sarita Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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7
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Sarkar S, Chandra Singh P. Spectroscopic and Simulation Studies of the Sequence-Dependent DNA Destabilization by a Fungicide. ACS OMEGA 2021; 6:14371-14378. [PMID: 34124459 PMCID: PMC8190899 DOI: 10.1021/acsomega.1c01228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/17/2021] [Indexed: 05/08/2023]
Abstract
The understanding of the structural change of DNA induced by fungicides is essential as the non-targeted action of fungicides causes genotoxicity, leading to several serious diseases such as cancer, behavioral change, and nausea. In this study, the binding of an important fungicide, namely, n-dodecylguanidine acetate (dodine), with B-DNA having different sequences of nucleobases and its effect on the structure of B-DNA has been investigated using spectroscopic and simulation methods. In general, the addition of dodine destabilizes DNA; however, the binding of dodine causing the destabilization of DNA is highly sequence dependent. In the case of adenine(A)-thymine(T)-based DNA, dodine intrudes into the minor groove of DNA and interacts with the A-T bases mainly through its hydrocarbon tail, which destabilizes the stacking interaction of the flanking bases. In contrast, the polar group of dodine interacts with guanine(G)-cytosine(C)-rich DNA, and the interaction is dynamic as it shuttles between the minor groove and terminal regions. The binding of dodine with G-C-rich DNA affects the stacking interaction of the terminal base regions specifically. This study reveals the base-specific binding mode of dodine, which causes destabilization of the duplex DNA.
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Doležel J, Lucretti S, Molnár I, Cápal P, Giorgi D. Chromosome analysis and sorting. Cytometry A 2021; 99:328-342. [PMID: 33615737 PMCID: PMC8048479 DOI: 10.1002/cyto.a.24324] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Flow cytometric analysis and sorting of plant mitotic chromosomes has been mastered by only a few laboratories worldwide. Yet, it has been contributing significantly to progress in plant genetics, including the production of genome assemblies and the cloning of important genes. The dissection of complex genomes by flow sorting into the individual chromosomes that represent small parts of the genome reduces DNA sample complexity and streamlines projects relying on molecular and genomic techniques. Whereas flow cytometric analysis, that is, chromosome classification according to fluorescence and light scatter properties, is an integral part of any chromosome sorting project, it has rarely been used on its own due to lower resolution and sensitivity as compared to other cytogenetic methods. To perform chromosome analysis and sorting, commercially available electrostatic droplet sorters are suitable. However, in order to resolve and purify chromosomes of interest the instrument must offer high resolution of optical signals as well as stability during long runs. The challenge is thus not the instrumentation, but the adequate sample preparation. The sample must be a suspension of intact mitotic metaphase chromosomes and the protocol, which includes the induction of cell cycle synchrony, accumulation of dividing cells at metaphase, and release of undamaged chromosomes, is time consuming and laborious and needs to be performed very carefully. Moreover, in addition to fluorescent staining chromosomal DNA, the protocol may include specific labelling of DNA repeats to facilitate discrimination of particular chromosomes. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flow-sorted fractions, and their suitability for downstream applications.
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Affiliation(s)
- Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Sergio Lucretti
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Debora Giorgi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
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Sarkar S, Chandra Singh P. Anions of Ionic Liquids Are Important Players in the Rescue of DNA Damage. J Phys Chem Lett 2020; 11:10150-10156. [PMID: 33191753 DOI: 10.1021/acs.jpclett.0c03016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The non-targeted action of fungicides generates genotoxic effect in vertebrates by perturbing the structure of DNA, which impacts its replication and transcriptional process, leading to several serious gene associated diseases. Hence, finding a suitable medium that can reduce/reverse the structural perturbation of DNA induced by fungicide, viz. dodine, is essential. Spectroscopic as well as molecular dynamics simulation techniques have been implemented to understand the effect of ionic liquids (ILs) having a tetramethylguanidinium cation along with short and long hydrophobic chain anions mixed with fungicide. The addition of ILs possessing anions with long hydrophobic chain blocks the fungicide from binding in the groove region of DNA by forming micelle-like structure and reverses the structural change induced by the fungicide. The hydrophobicity of long hydrocarbon and fluorocarbon chains of anions is a key parameter for reversing the effect of fungicide as small anion based ILs are incapable of annulling the structural change of DNA.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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Vallmitjana A, Torrado B, Dvornikov A, Ranjit S, Gratton E. Blind Resolution of Lifetime Components in Individual Pixels of Fluorescence Lifetime Images Using the Phasor Approach. J Phys Chem B 2020; 124:10126-10137. [PMID: 33140960 DOI: 10.1021/acs.jpcb.0c06946] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phasor approach is used in fluorescence lifetime imaging microscopy for several purposes, notably to calculate the metabolic index of single cells and tissues. An important feature of the phasor approach is that it is a fit-free method allowing immediate and easy to interpret analysis of images. In a recent paper, we showed that three or four intensity fractions of exponential components can be resolved in each pixel of an image by the phasor approach using simple algebra, provided the component phasors are known. This method only makes use of the rule of linear combination of phasors rather than fits. Without prior knowledge of the components and their single exponential decay times, resolution of components and fractions is much more challenging. Blind decomposition has been carried out only for cuvette experiments wherein the statistics in terms of the number of photons collected is very good. In this paper, we show that using the phasor approach and measurements of the decay at phasor harmonics 2 and 3, available using modern electronics, we could resolve the decay in each pixel of an image in live cells or mice liver tissues with two or more exponential components without prior knowledge of the values of the components. In this paper, blind decomposition is achieved using a graphical method for two components and a minimization method for three components. This specific use of the phasor approach to resolve multicomponents in a pixel enables applications where multiplexing species with different lifetimes and potentially different spectra can provide a different type of super-resolved image content.
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Affiliation(s)
- Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Belén Torrado
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
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Sarkar S, Singh PC. Sequence specific hydrogen bond of DNA with denaturants affects its stability: Spectroscopic and simulation studies. Biochim Biophys Acta Gen Subj 2020; 1865:129735. [PMID: 32946929 DOI: 10.1016/j.bbagen.2020.129735] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/21/2020] [Accepted: 09/13/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Several different small molecules have been used to target the DNA helix in order to treat the diseases caused by its mutation. Guanidinium(Gdm+) and urea based drugs have been used for the diseases related to central nervous system, also as the anti-inflammatory and chemotherapeutic agent. However, the role of Gdm+ and urea in the stabilization/destabilization of DNA is not well understood. METHODS Spectroscopic techniques along with molecular dynamics (MD) simulation have been performed on different sequences of DNA in the presence of guanidinium chloride (GdmCl) and urea to decode the binding of denaturants with DNA and the role of hydrogen bond with the different regions of DNA in its stability/destability. RESULTS AND CONCLUSION Our study reveals that, Gdm+ of GdmCl and urea both intrudes into the groove region of DNA along with the interaction with its phosphate backbone. However, interaction of Gdm+ and urea with the nucleobases in the groove region is different. Gdm+ forms the intra-strand hydrogen bond with the central region of the both sequences of DNA whereas inter-strand hydrogen bond along with water assisted hydrogen bond takes place in the case of urea. The intra-strand hydrogen bond formation capability of Gdm+ with the nucleobases in the minor groove of DNA decreases its groove width which probably causes the stabilization of B-DNA in GdmCl. In contrast, the propensity of the formation of inter-strand hydrogen bond of urea with the nucleobases in the groove region of DNA without affecting the groove width destabilizes B-DNA as compared to GdmCl. This study depicts that the opposite effect of GdmCl and urea on the stability is a general property of B-DNA. However, the extent of stabilization/destabilization of DNA in Gdm+ and urea depend on its sequence probably due to the difference in the intra/inter-strand hydrogen bonding with different bases present in both the sequences of DNA. GENERAL SIGNIFICANCE The information obtained from this study will be useful for the designing of Gdm+ based drug molecule which can target the DNA more specifically and selectively.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 70032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 70032, India.
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12
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Sarkar S, Rajdev P, Singh PC. Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies. Phys Chem Chem Phys 2020; 22:15582-15591. [PMID: 32613973 DOI: 10.1039/d0cp01548b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ionic liquids (ILs) have been extensively used for stabilization and long-term DNA storage. However, molecular level understanding of the role of the hydrogen bond of DNA with ILs in its stabilization is still inadequate. Two ILs, namely, 1,1,3,3-tetramethylguanidinium acetate (TMG) and 2,2-diethyl-1,1,3,3-tetramethylguanidinium acetate (DETMG), have been synthesized, of which TMG has a hydrogen bonding N-H group whereas DETMG does not contain any hydrogen bonding site. It has been found that both TMG and DETMG cations interact in the groove region of DNA; however, their mode of interaction is distinctly different, which causes the stabilization of DNA in the presence of TMG, whereas the effect is opposite in the case of DETMG. It is apparent from the data that only the accommodation of ILs in the groove region is not enough for the stabilization of DNA. MD simulation and spectroscopic studies combinedly indicate that the hydrogen bonding capability of the TMG cation enhances the hydrogen bonding between the Watson-Crick base pairs of DNA, resulting in its stabilization. In contrast, the bigger size as well as the absence of the hydrogen bonding site of the DETMG cation perturbs the minor groove width and base pair step parameters of DNA during its intrusion into the minor groove, which decreases the hydrogen bond between the Watson-Crick base pairs of DNA, leading to destabilization.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
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13
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Sarkar S, Singh PC. Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability. Biochim Biophys Acta Gen Subj 2020; 1864:129498. [DOI: 10.1016/j.bbagen.2019.129498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023]
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14
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Piriyakarnsakul S, Takarada K, Heab KE, Nasu M, Hata M, Furuuchi M. Optimal fluorescent-dye staining time for the real-time detection of microbes: a study of Saccharomyces cerevisiae. J Appl Microbiol 2020; 128:1694-1702. [PMID: 31925843 DOI: 10.1111/jam.14577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/27/2019] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
AIMS To provide information on the time-dependent behaviour of microbe staining by fluorescent dyes in the order of seconds, which is important in terms of the recent rapid and online techniques for microbe measurements and/or environmental microbe analysis. METHODS AND RESULTS For combinations of yeast (Saccharomyces cerevisiae) and typical dyes, including DAPI (4',6-diamidino-2-phenylindole) and Auramine-O, a suspension of yeast cells in ultrapure water was injected into a dye solution in a micro cuvette placed inside a spectrofluorometer and the fluorescence intensity of the resulting solution was measured at 1 s intervals, starting immediately after the mixing and continued until the time for the maximum intensity using various concentrations of yeast and dyes. The relaxation time τ, which corresponds to ~63·2% of the maximum fluorescence intensity, was shown to decrease to below 1 s with increasing DAPI concentration, whereas it remained constant for 2-3 s with increasing Auramine-O concentration, for example at a yeast concentration of 100 µg ml-1 . CONCLUSIONS For the conditions of yeast >10 µg ml-1 , DAPI >1 µg ml-1 and Auramine-O >0·1 µg ml-1 , τ could be adjusted to below 5 s to achieve a rapid and stable staining. SIGNIFICANCE AND IMPACT OF THE STUDY Design and operating conditions for rapid and online measurements of microbes can be optimized.
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Affiliation(s)
- S Piriyakarnsakul
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - K Takarada
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - K E Heab
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - M Nasu
- Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - M Hata
- Faculty of Geoscience and Civil Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - M Furuuchi
- Faculty of Geoscience and Civil Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,Faculty of Environmental Management, Prince of Songkla University, Hat Yai, Thailand
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15
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Steuwe C, Vaeyens MM, Jorge-Peñas A, Cokelaere C, Hofkens J, Roeffaers MBJ, Van Oosterwyck H. Fast quantitative time lapse displacement imaging of endothelial cell invasion. PLoS One 2020; 15:e0227286. [PMID: 31910228 PMCID: PMC6946139 DOI: 10.1371/journal.pone.0227286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
In order to unravel rapid mechano-chemical feedback mechanisms in sprouting angiogenesis, we combine selective plane illumination microscopy (SPIM) and tailored image registration algorithms - further referred to as SPIM-based displacement microscopy - with an in vitro model of angiogenesis. SPIM successfully tackles the problem of imaging large volumes while upholding the spatial resolution required for the analysis of matrix displacements at a subcellular level. Applied to in vitro angiogenic sprouts, this unique methodological combination relates subcellular activity - minute to second time scale growing and retracting of protrusions - of a multicellular systems to the surrounding matrix deformations with an exceptional temporal resolution of 1 minute for a stack with multiple sprouts simultaneously or every 4 seconds for a single sprout, which is 20 times faster than with a conventional confocal setup. Our study reveals collective but non-synchronised, non-continuous activity of adjacent sprouting cells along with correlations between matrix deformations and protrusion dynamics.
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Affiliation(s)
- Christian Steuwe
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, Belgium
| | - Marie-Mo Vaeyens
- Biomechanics Section (BMe), Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Alvaro Jorge-Peñas
- Biomechanics Section (BMe), Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Célie Cokelaere
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, Belgium
| | - Johan Hofkens
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Maarten B. J. Roeffaers
- Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions (cMACS), Department of Microbial and Molecular Systems (MS), KU Leuven, Leuven, Belgium
| | - Hans Van Oosterwyck
- Biomechanics Section (BMe), Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
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16
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Gatadi S, Pulivendala G, Gour J, Malasala S, Bujji S, Parupalli R, Shaikh M, Godugu C, Nanduri S. Synthesis and evaluation of new 4(3H)-Quinazolinone derivatives as potential anticancer agents. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Mora AK, Khan S, Patro BS, Nath S. Is DAPI assay of cellular nucleic acid reliable in the presence of protein aggregates? Chem Commun (Camb) 2020; 56:13844-13847. [DOI: 10.1039/d0cc04108d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Intracellular amyloid fibrils prevent exclusive staining of nuclei by DAPI.
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Affiliation(s)
- Aruna K. Mora
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
| | - Sufiyan Khan
- Ramnarain Ruia Autonomous College
- Mumbai 400 019
- India
| | - Birija S. Patro
- Homi Bhabha National Institute
- Mumbai 400 094
- India
- Bio-Organic Division
- Bhabha Atomic Research Centre
| | - Sukhendu Nath
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
- Homi Bhabha National Institute
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18
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Sarkar S, Chowdhury A, Singh PC. Multimodal Interactions of Dopamine Hydrochloride with the Groove Region of DNA: A Key Factor in the Enhanced Stability of DNA. J Phys Chem B 2019; 123:10700-10708. [DOI: 10.1021/acs.jpcb.9b09254] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhinanda Chowdhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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19
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Sarkar S, Singh PC. Mechanistic Aspects of Fungicide-Induced DNA Damage: Spectroscopic and Molecular Dynamics Simulation Studies. J Phys Chem B 2019; 123:8653-8661. [DOI: 10.1021/acs.jpcb.9b06009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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20
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Yahav G, Diamandi HH, Preter E, Fixler D. The squared distance approach to frequency domain time-resolved fluorescence analysis. JOURNAL OF BIOPHOTONICS 2019; 12:e201800485. [PMID: 30809961 DOI: 10.1002/jbio.201800485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/24/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
A frequency-domain (FD) analysis of fluorescence lifetime (FLT) is a unique and rapid method for cellular and intracellular classifications that can serve for medical diagnostics purposes. Nevertheless, its data analysis process demands nonlinear fitting algorithms that may distort the resolution of the FLT data and hence diminish the classification ability of the method. This research suggests a sample classification technique that is unaffected by the analysis process as it is based on the squared distance (D2 ) between the raw frequency response data (FRD). In addition, it presents the theory behind this technique and its validation in two simulated data sets of six groups with similar widely and closely spaced FLT data as well as in experimental data of 43 samples from bacterial and viral infected and non-infected patients. In the two simulated tests, the classification accuracy was above 95% for all six groups. In the experimental data, the classification of 41 out of 43 samples matched earlier report and 29 out of 31 agreed with preliminary physician diagnosis. The D2 approach has the potential to promote FD-time resolved fluorescence measurements as a medical diagnostic technique with high specifity and high sensitivity for many of today's conventional diagnostic procedures.
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Affiliation(s)
- Gilad Yahav
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Hilel H Diamandi
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Eyal Preter
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dror Fixler
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
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21
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Quantification of fixed adherent cells using a strong enhancer of the fluorescence of DNA dyes. Sci Rep 2019; 9:8701. [PMID: 31213648 PMCID: PMC6581942 DOI: 10.1038/s41598-019-45217-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/04/2019] [Indexed: 01/08/2023] Open
Abstract
Cell quantification is widely used in basic or applied research. The current sensitive methods of cell quantification are exclusively based on the analysis of non-fixed cells and do not allow the simultaneous detection of various cellular components. A fast, sensitive and cheap method of the quantification of fixed adherent cells is described here. It is based on the incubation of DAPI- or Hoechst 33342-stained cells in a solution containing SDS. The presence of SDS results in the quick de-staining of DNA and simultaneously, in an up-to-1,000-fold increase of the fluorescence intensity of the used dyes. This increase can be attributed to the micelle formation of SDS. The method is sufficiently sensitive to reveal around 50–70 human diploid cells. It is compatible with immunocytochemical detections, the detection of DNA replication and cell cycle analysis by image cytometry. The procedure was successfully tested for the analysis of cytotoxicity. The method is suitable for the quantification of cells exhibiting low metabolic activity including senescent cells. The developed procedure provides high linearity and the signal is high for at least 20 days at room temperature. Only around 90 to 120 minutes is required for the procedure’s completion.
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22
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Zhang S, Assaf KI, Huang C, Hennig A, Nau WM. Ratiometric DNA sensing with a host-guest FRET pair. Chem Commun (Camb) 2019; 55:671-674. [PMID: 30565597 DOI: 10.1039/c8cc09126a] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A supramolecular host-guest FRET pair based on a carboxyfluorescein-labelled cucurbit[7]uril (CB7-CF, as acceptor) and the fluorescent dye 4',6-diamidino-2-phenylindole (DAPI, as donor) is developed for sensing of DNA. In comparison to the commercial DNA staining dye SYBR Green I, the new chemosensing ensemble offers dual-emission signals, which allows a linear ratiometric response over a wide concentration range.
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Affiliation(s)
- Shuai Zhang
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany.
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23
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Bellam R, Jaganyi D, Mambanda A, Robinson R, BalaKumaran MD. Seven membered chelate Pt(ii) complexes with 2,3-di(2-pyridyl)quinoxaline ligands: studies of substitution kinetics by sulfur donor nucleophiles, interactions with CT-DNA, BSA and in vitro cytotoxicity activities. RSC Adv 2019; 9:31877-31894. [PMID: 35530785 PMCID: PMC9072748 DOI: 10.1039/c9ra06488e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/18/2019] [Indexed: 11/21/2022] Open
Abstract
Dichloro platinum(ii) complexes coordinated with 2,3-di(2-pyridyl)quinoxaline ligands which form seven-membered chelates namely, bpqPtCl2, dmbpqPtCl2 and bbqPtCl2 (where bpq, dmbpq and bbq are 2,3-di(2-pyridyl)quinoxaline, 6,7-dimethyl-2,3-di(2-pyridyl)quinoxaline and 2,3-bis(2′pyriyl)benzo[g]quinoxaline, respectively) were synthesized, characterised and their respective hydrated product complexes namely, bpqPt(OH2)22+, dmbpqPt(OH2)22+ and bbqPt(OH2)22+ were prepared by chloride metathesis. The substitution kinetics of the aquated cations by thiourea nucleophiles indicated that the two aqua ligands are substituted simultaneously according to the rate law: kobs = k2[Nu]. This is followed by a forced dechelation of the ligands from the Pt (II) to form Pt(Nu)42+ species. The dechelation step is considerably slow to be monitored reliably. The rate of substitution is marginally enhanced by introducing two methyl groups and by extending the π-conjugation on the bpq core ligand. The reactivity order increased as bpqPt(OH2)22+ < dmbpqPt(OH2)22+ < bbqPt(OH2)22+. Reactivity trends were well supported by theoretical computed DFT electronic descriptors. The interactions of the Pt(ii) complexes with CT-DNA and BSA were also examined spectroscopically in tris buffers at pH 7.2. Spectroscopic and viscosity measurements suggested strong associative interactions between the Pt(ii) complexes and CT-DNA, most likely through groove binding. In silico theoretical binding studies showed energetically stable poses through associative non-covalent interactions. In vitro MTT cytotoxicity IC50 values of the Pt(ii) complexes on human liver carcinoma cells (HepG2) cancer cell lines revealed bbqPtCl2 as the least active. The fluorescence staining assays revealed the morphological changes suggested early apoptotic induction as well as non-specific necrosis. Dichloro platinum(ii) complexes coordinated with 2,3-di(2-pyridyl)quinoxaline ligands form seven-membered chelates were synthesized, characterised and their respective hydrated product complexes were prepared by chloride metathesis.![]()
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Affiliation(s)
- Rajesh Bellam
- School of Chemistry and Physics
- University of KwaZulu-Natal
- Pietermaritzburg 3209
- South Africa
| | - Deogratius Jaganyi
- School of Science
- College of Science and Technology
- University of Rwanda
- Kigali
- Rwanda
| | - Allen Mambanda
- School of Chemistry and Physics
- University of KwaZulu-Natal
- Pietermaritzburg 3209
- South Africa
| | - Ross Robinson
- School of Chemistry and Physics
- University of KwaZulu-Natal
- Pietermaritzburg 3209
- South Africa
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24
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Sekhar AR, Mallik B, Kumar V, Sankar J. A cell-permeant small molecule for the super-resolution imaging of the endoplasmic reticulum in live cells. Org Biomol Chem 2019; 17:3732-3736. [DOI: 10.1039/c9ob00408d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A simple BODIPY-based small molecule has been identified to selectively label the endoplasmic reticulum for high-resolution imaging with negligible cytotoxicity.
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Affiliation(s)
- Adiki Raja Sekhar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- India
| | - Bhagaban Mallik
- Laboratory of Neurogenetics
- Department of Biological Sciences
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- India
| | - Vimlesh Kumar
- Laboratory of Neurogenetics
- Department of Biological Sciences
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- India
| | - Jeyaraman Sankar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- India
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25
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Yahav G, Gershanov S, Salmon-Divon M, Ben-Zvi H, Mircus G, Goldenberg-Cohen N, Fixler D. Pathogen Detection Using Frequency Domain Fluorescent Lifetime Measurements. IEEE Trans Biomed Eng 2018; 65:2731-2741. [PMID: 29993446 DOI: 10.1109/tbme.2018.2814597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Inflammation of the meninges is a source of severe morbidity and therefore is an important health concerns worldwide. The conventional clinical microbiology approaches used today to identify pathogens suffer from several drawbacks and frequently provide false results. This research describes a fast method to detect the presence of pathogens using the frequency domain (FD) fluorescence lifetime (FLT) imaging microscopy (FLIM) system. METHODS The study included 43 individuals divided into 4 groups: 9 diagnosed with different types of bacteria; 16 diagnosed with different types of viruses; 5 healthy samples served as a control; and 12 samples were negative to any pathogen, although presenting related symptoms. All samples contained leukocytes that were extracted from the cerebrospinal fluid (CSF) and were subjected to nuclear staining by 4', 6-diamidino-2-phenylindole (DAPI) and FLT analyses based on phase and amplitude crossing point (CRPO). RESULTS Using notched boxplots, we found differences in 95% probability between the first three groups through different notch ranges (NR). Pathogen samples presented a longer median FLT (3.28 ns with NR of 3.24-3.32 ns in bacteria and 3.18 ns with NR of 3.16-3.21 ns in viruses) compared to the control median FLT (2.65 ns with NR of 2.63-2.67 ns). Furthermore, we found that the undetected forth group was divided into two types: a relatively normal median FLT (2.72 ns with NR of 2.68-2.76 ns) and a prolonged FLT (3.22 ns with NR of 3.17-3.27 ns). CONCLUSION FLT measurements can differentiate between control and pathogen by the CRPO method. SIGNIFICANCE The FD-FLIM system can provide a high throughput diagnostic technique that does not require a physician.
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26
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Prajapati R, Mukherjee TK. Effect of surfactant assemblies on the resonance energy transfer from 4′,6-diamidino-2-phenylindole to silver nanoclusters. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Abstract
DNA diffusion assay is a simple, sensitive and reliable technique which allows the assessment of programmed cell death (PCD) or necrosis events based on nuclear morphology. It consists in isolating nuclei from plant material, which are then embedded in agarose and subjected to lysis in alkaline buffers. Under these conditions, and due to the presence of abundant alkali-labile sites in the DNA, small pieces of DNA diffuse in the agarose gel giving a specific halo appearance when stained with fluorescent dyes like DAPI (4',6-diamidino-2-phenylindole). Here, we describe an optimized protocol for DNA diffusion assay applied to different types of plant cells/tissues, indicating all the critical steps required for a successful experimental procedure.
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Affiliation(s)
- Anca Macovei
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, Italy
| | - Mattia Donà
- Gregor Mendel Institute (GMI), Vienna Biocenter (VBC), Austrian Academy of Science, Vienna, Austria
| | - Daniela Carbonera
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', University of Pavia, Pavia, Italy.
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28
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Wang Y, Sischka A, Walhorn V, Tönsing K, Anselmetti D. Nanomechanics of Fluorescent DNA Dyes on DNA Investigated by Magnetic Tweezers. Biophys J 2017; 111:1604-1611. [PMID: 27760348 DOI: 10.1016/j.bpj.2016.08.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/29/2016] [Accepted: 08/26/2016] [Indexed: 11/25/2022] Open
Abstract
Fluorescent DNA dyes are broadly used in many biotechnological applications for detecting and imaging DNA in cells and gels. Their binding alters the structural and nanomechanical properties of DNA and affects the biological processes that are associated with it. Although interaction modes like intercalation and minor groove binding already have been identified, associated mechanic effects like local elongation, unwinding, and softening of the DNA often remain in question. We used magnetic tweezers to quantitatively investigate the impact of three DNA-binding dyes (YOYO-1, DAPI, and DRAQ5) in a concentration-dependent manner. By extending and overwinding individual, torsionally constrained, nick-free dsDNA molecules, we measured the contour lengths and molecular forces that allow estimation of thermodynamic and nanomechanical binding parameters. Whereas for YOYO-1 and DAPI the binding mechanisms could be assigned to bis-intercalation and minor groove binding, respectively, DRAQ5 exhibited both binding modes in a concentration-dependent manner.
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Affiliation(s)
- Ying Wang
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany
| | - Andy Sischka
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany
| | - Volker Walhorn
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany
| | - Katja Tönsing
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany
| | - Dario Anselmetti
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany.
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29
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Gershanov S, Michowiz S, Toledano H, Yahav G, Barinfeld O, Hirshberg A, Ben-Zvi H, Mircus G, Salmon-Divon M, Fixler D, Goldenberg-Cohen N. Fluorescence Lifetime Imaging Microscopy, a Novel Diagnostic Tool for Metastatic Cell Detection in the Cerebrospinal Fluid of Children with Medulloblastoma. Sci Rep 2017. [PMID: 28623325 PMCID: PMC5473849 DOI: 10.1038/s41598-017-03892-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In pediatric brain tumours, dissemination of malignant cells within the central nervous system confers poor prognosis and determines treatment intensity, but is often undetectable by imaging or cytology. This study describes the use of fluorescence lifetime (FLT) imaging microscopy (FLIM), a novel diagnostic tool, for detection of metastatic spread. The study group included 15 children with medulloblastoma and 2 with atypical teratoid/rhabdoid tumour. Cells extracted from the tumour and the cerebrospinal fluid (CSF) 2 weeks postoperatively and repeatedly during chemo/radiotherapy were subjected to nuclear staining followed by FLT measurement and cytological study. Control CSF samples were collected from patients with infectious/inflammatory disease attending the same hospital. Median FLT was prolonged in tumour cells (4.27 ± 0.28 ns; P < 2.2*10−16) and CSF metastatic cells obtained before chemo/radiotherapy (6.28 ± 0.22 ns; P < 2.2*10−16); normal in inflammatory control cells (2.6 ± 0.04 ns) and cells from children without metastasis before chemo/radiotherapy (2.62 ± 0.23 ns; P = 0.858) and following treatment (2.62 ± 0.21 ns; P = 0.053); and short in CSF metastatic cells obtained after chemo/radiotherapy (2.40 ± 0.2 ns; P < 2.2*10−16). FLIM is a simple test that can potentially identify CSF spread of brain tumours. FLT changes in accordance with treatment, with significant prolonged median values in tumours and metastases. More accurate detection of metastatic cells may guide personalised treatment and improve the therapeutic outcome.
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Affiliation(s)
- Sivan Gershanov
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, 40700, Israel.,The Krieger Eye Research Laboratory, Felsenstein Medical Research Center, Beilinson Hospital, Petach Tikva 4941492, affiliated to Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shalom Michowiz
- Department of Pediatric Neurosurgery, Schneider Children's Medical Center of Israel, Petach Tikva, 4920235, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Helen Toledano
- Department of Pediatric Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, 4920235, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gilad Yahav
- Faculty of Engineering and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Orit Barinfeld
- The Krieger Eye Research Laboratory, Felsenstein Medical Research Center, Beilinson Hospital, Petach Tikva 4941492, affiliated to Tel Aviv University, Tel Aviv, 6997801, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Avraham Hirshberg
- Department of Oral Pathology and Oral Medicine, Maurice and Gabriela Goldschleger School of Dental Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Haim Ben-Zvi
- Laboratory of Microbiology, Rabin Medical Center - Beilinson Hospital, Petach Tikva, 4941492, Israel
| | - Gabriel Mircus
- Laboratory of Microbiology, Rabin Medical Center - Beilinson Hospital, Petach Tikva, 4941492, Israel
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, 40700, Israel
| | - Dror Fixler
- Faculty of Engineering and Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Nitza Goldenberg-Cohen
- The Krieger Eye Research Laboratory, Felsenstein Medical Research Center, Beilinson Hospital, Petach Tikva 4941492, affiliated to Tel Aviv University, Tel Aviv, 6997801, Israel. .,Department of Ophthalmology, Bnai Zion Medical Center, Haifa, 3339419, Israel.
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30
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Jana TK, Pal A, Mandal AK, Sarwar S, Chakrabarti P, Chatterjee K. Photocatalytic and Antibacterial Performance of α-Fe2
O3
Nanostructures. ChemistrySelect 2017. [DOI: 10.1002/slct.201700294] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- T. K. Jana
- Dept of Physics and Technophysics; Vidyasagar University; Midnapore - 721102 India
| | - A. Pal
- Dept of Physics and Technophysics; Vidyasagar University; Midnapore - 721102 India
| | - A. K. Mandal
- Chemical Biology Laboratory; Dept. of Sericulture; Raiganj University; Raiganj - 733134 India
| | - S. Sarwar
- Department of Biochemistry; Bose Institute; Kolkata 700054 India
| | - P. Chakrabarti
- Department of Biochemistry; Bose Institute; Kolkata 700054 India
| | - K. Chatterjee
- Dept of Physics and Technophysics; Vidyasagar University; Midnapore - 721102 India
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31
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Wang Y, Schellenberg H, Walhorn V, Toensing K, Anselmetti D. Binding Mechanism of Fluorescent Dyes to DNA Characterized by Magnetic Tweezers. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.matpr.2017.09.190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Sharma P, Srinivasa Reddy T, Thummuri D, Senwar KR, Praveen Kumar N, Naidu V, Bhargava SK, Shankaraiah N. Synthesis and biological evaluation of new benzimidazole-thiazolidinedione hybrids as potential cytotoxic and apoptosis inducing agents. Eur J Med Chem 2016; 124:608-621. [DOI: 10.1016/j.ejmech.2016.08.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/01/2016] [Accepted: 08/14/2016] [Indexed: 01/11/2023]
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33
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Kasyanenko N, Bakulev V, Perevyazko I, Nekrasova T, Nazarova O, Slita A, Zolotova Y, Panarin E. Model system for multifunctional delivery nanoplatforms based on DNA-Polymer complexes containing silver nanoparticles and fluorescent dye. J Biotechnol 2016; 236:78-87. [DOI: 10.1016/j.jbiotec.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/07/2016] [Accepted: 08/12/2016] [Indexed: 10/21/2022]
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34
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Yahav G, Hirshberg A, Salomon O, Amariglio N, Trakhtenbrot L, Fixler D. Fluorescence lifetime imaging of DAPI-stained nuclei as a novel diagnostic tool for the detection and classification of B-cell chronic lymphocytic leukemia. Cytometry A 2016; 89:644-52. [DOI: 10.1002/cyto.a.22890] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/21/2016] [Accepted: 05/18/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Gilad Yahav
- Faculty of Engineering and Institute of Nanotechnology and Advanced Materials; Bar Ilan University; Ramat Gan Israel
| | - Abraham Hirshberg
- Department of Oral Pathology and Oral Medicine, Maurice and Gabriela Goldschleger School of Dental Medicine; Tel Aviv University; Tel Aviv Israel
| | - Ophira Salomon
- Thrombosis Unit, Sheba Medical Center and Sackler Faculty of Medicine; Tel Aviv University; Tel Aviv Israel
| | | | | | - Dror Fixler
- Faculty of Engineering and Institute of Nanotechnology and Advanced Materials; Bar Ilan University; Ramat Gan Israel
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Haines AM, Linacre A. A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling. Forensic Sci Int 2016; 262:190-5. [DOI: 10.1016/j.forsciint.2016.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/16/2016] [Accepted: 03/12/2016] [Indexed: 12/24/2022]
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Datz S, Argyo C, Gattner M, Weiss V, Brunner K, Bretzler J, von Schirnding C, Torrano AA, Spada F, Vrabel M, Engelke H, Bräuchle C, Carell T, Bein T. Genetically designed biomolecular capping system for mesoporous silica nanoparticles enables receptor-mediated cell uptake and controlled drug release. NANOSCALE 2016; 8:8101-8110. [PMID: 27021414 DOI: 10.1039/c5nr08163g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Effective and controlled drug delivery systems with on-demand release and targeting abilities have received enormous attention for biomedical applications. Here, we describe a novel enzyme-based cap system for mesoporous silica nanoparticles (MSNs) that is directly combined with a targeting ligand via bio-orthogonal click chemistry. The capping system is based on the pH-responsive binding of an aryl-sulfonamide-functionalized MSN and the enzyme carbonic anhydrase (CA). An unnatural amino acid (UAA) containing a norbornene moiety was genetically incorporated into CA. This UAA allowed for the site-specific bio-orthogonal attachment of even very sensitive targeting ligands such as folic acid and anandamide. This leads to specific receptor-mediated cell and stem cell uptake. We demonstrate the successful delivery and release of the chemotherapeutic agent Actinomycin D to KB cells. This novel nanocarrier concept provides a promising platform for the development of precisely controllable and highly modular theranostic systems.
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Affiliation(s)
- Stefan Datz
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Christian Argyo
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Michael Gattner
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Veronika Weiss
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Korbinian Brunner
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Johanna Bretzler
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Constantin von Schirnding
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Adriano A Torrano
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Fabio Spada
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Milan Vrabel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic
| | - Hanna Engelke
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Christoph Bräuchle
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Thomas Carell
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Thomas Bein
- Department of Chemistry, Nanosystems Initiative Munich (NIM), Center for Nano Science (CeNS), and Center for Integrated Protein Science Munich (CIPSM), University of Munich (LMU), Butenandtstr. 5-13, 81377 Munich, Germany.
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Haines AM, Tobe SS, Kobus H, Linacre A. Successful direct STR amplification of hair follicles after nuclear staining. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Haines AM, Tobe SS, Kobus H, Linacre A. Finding DNA: Using fluorescent in situ detection. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.198] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Haines AM, Tobe SS, Kobus HJ, Linacre A. Effect of nucleic acid binding dyes on DNA extraction, amplification, and STR typing. Electrophoresis 2015. [DOI: 10.1002/elps.201500170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alicia M. Haines
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Shanan S. Tobe
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Hilton J. Kobus
- School of Chemical and Physical Sciences; Flinders University; Adelaide South Australia
| | - Adrian Linacre
- School of Biological Sciences; Flinders University; Adelaide South Australia
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40
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Antibacterial and DNA degradation potential of silver nanoparticles synthesized via green route. Int J Biol Macromol 2015; 80:455-9. [DOI: 10.1016/j.ijbiomac.2015.07.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 06/24/2015] [Accepted: 07/12/2015] [Indexed: 11/15/2022]
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41
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Pabbathi A, Samanta A. Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid. J Phys Chem B 2015; 119:11099-105. [PMID: 26061788 DOI: 10.1021/acs.jpcb.5b02939] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural integrity of a nucleic acid under various conditions determines its utility in biocatalysis and biotechnology. Exploration of the ionic liquids (ILs) for extraction of DNA and other nucleic acid based applications requires an understanding of the nature of interaction between the IL and DNA. Considering these aspects, we have studied the interaction between calf-thymus DNA and a less toxic morpholinium IL, [Mor1,2][Br], employing fluorescence correlation spectroscopy (FCS), conventional steady state and time-resolved fluorescence, circular dichroism (CD) and molecular docking techniques. While the CD spectra indicate the stability of DNA and retention of its B-form in the presence of the morpholinium IL, the docking study reveals that [Mor1,2](+) binds to the minor groove of DNA with a binding energy of -4.57 kcal mol(-1). The groove binding of the cationic component of the IL is corroborated by the steady state fluorescence data, which indicated displacement of a known minor groove binder, DAPI, from its DNA-bound state on addition of [Mor1,2][Br]. The FCS measurements show that the hydrodynamic radius of DNA remains more or less constant in the presence of [Mor1,2][Br], thus suggesting that the structure of DNA is retained in the presence of the IL. DNA melting experiments show that the thermal stability of DNA is enhanced in the presence of morpholinium IL.
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Affiliation(s)
- Ashok Pabbathi
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
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42
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Green synthesis of silver nanoparticles using glucan from mushroom and study of antibacterial activity. Int J Biol Macromol 2013; 62:439-49. [DOI: 10.1016/j.ijbiomac.2013.09.019] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/26/2013] [Accepted: 09/19/2013] [Indexed: 11/17/2022]
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Biancardi A, Biver T, Secco F, Mennucci B. An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools. Phys Chem Chem Phys 2013; 15:4596-603. [PMID: 23423468 DOI: 10.1039/c3cp44058c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.
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Affiliation(s)
- Alessandro Biancardi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento, 35-56126 Pisa, Italy.
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Shin YC, Lee JH, Jeong JE, Kim B, Lee EJ, Jin OS, Jung TG, Lee JJ, Woo HY, Han DW. Cell imaging and DNA delivery in fibroblastic cells by conjugated polyelectrolytes. Biotechnol Appl Biochem 2013; 60:580-8. [PMID: 23772797 DOI: 10.1002/bab.1106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/06/2013] [Indexed: 12/23/2022]
Abstract
This study concentrates on the potential application of conjugated polyelectrolytes (CPEs) to cell imaging and DNA delivery. Four different types of polyfluorene copolymers, namely, PAHFP-Br, PAEFP-Br, PAHFbT-Br, and PSBFP-Na, which have the same π-conjugated backbone but different side chains, were synthesized. For cytotoxicity testing, L-929 fibroblastic cells were treated with increasing concentrations (0-50 µM) of each CPE and then cell viability was determined by WST-8 assay. Cellular uptake of CPEs into cultured L-929 cells was observed by fluorescence microscopy. To examine DNA delivery by CPEs, the cells were incubated for 1 H with PAHFP-Br/fluorescein (Fl)-labeled single-stranded DNA (ssDNA-Fl) complex and then visualized by fluorescence microscopy. Cytotoxicity of CPEs was increased in a dose-dependent manner but at lower than 10 µM, PAHFP-Br, PAEFP-Br, and PSBFP-Na did not show any cytotoxic effects on the cells. When added to cell cultures at 1 µM, PAHFP-Br/ssDNA-Fl complex was delivered and then dissociated into PAHFP-Br and ssDNA-Fl within the cells. This result implies that PAHFP-Br can enable cell imaging and DNA delivery into fibroblastic cells. Therefore, it is suggested that PAHFP-Br with various advantages such as low cytotoxicity and high fluorescence efficiency can be extensively used as a potential agent for cell imaging and gene delivery.
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Affiliation(s)
- Yong Cheol Shin
- Department of Applied Nanoscience and Department of Nanofusion Technology (BK21), College of Nanoscience and Nanotechnology, Pusan National University, Busan, Korea
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Singh D, Vishnoi T, Kumar A. Effect of alpha-ketoglutarate on growth and metabolism of cells cultured on three-dimensional cryogel matrix. Int J Biol Sci 2013; 9:521-30. [PMID: 23781146 PMCID: PMC3677688 DOI: 10.7150/ijbs.4962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/11/2012] [Indexed: 11/17/2022] Open
Abstract
Alpha- ketoglutarate (α-KG) is a well-known intermediate of Kreb's cycle and thus one of the important candidates in the role of cellular metabolism. The aim was to investigate the effect of α-KG on the growth and proliferation of different cells (fibroblasts and chondrocytes). Further change in the consumption of glucose and release of ammonia in the media, upon the addition of α-KG was also examined. NIH3T3 and chondrocytes were seeded on two different macroporous cryogel matrices synthesized by poly (hydroxyethylmethaacrylate)-gelatin (HG) and alginate-gelatin (AG). Higher proliferation was observed for both the cell lines in 2-D as well as 3-D where α-KG was added to the media compared to the controls. It was evident that the chondrocytes were metabolically more active in the case of α-KG containing samples as early extracellular matrix (ECM) accumulation was observed. In comparison to the 6-8 weeks duration required by the chondrocytes for ECM accumulation in normal in-vitro culture conditions, α-KG containing samples showed an earlier accumulation within 3 weeks. In order to further validate the results, scanning electron microscopic (SEM) analysis was performed showed high ECM deposition and cells embedded in the matrix. Homogenous distribution of cells on both the synthesized matrix was reported using 4'-6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI) staining. The results clearly showed reduction in ammonia concentration in α-KG containing samples thus leading to decreased ammonia toxicity that builds up during long cell culture conditions thereby enhancing the proliferation and metabolic activity. Thus α-KG can be used potentially for long batch-cultures for the production of vaccines or antibody as well as can play an important role as a bioactive molecule for in vitro neo-cartilage generation.
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Affiliation(s)
- Deepti Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur-208016, UP, India
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46
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The hazards of DAPI photoconversion: effects of dye, mounting media and fixative, and how to minimize the problem. Histochem Cell Biol 2012; 139:195-204. [PMID: 23064788 DOI: 10.1007/s00418-012-1039-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2012] [Indexed: 10/27/2022]
Abstract
Immunocytochemistry is a powerful tool for detection and visualization of specific molecules in living or fixed cells, their localization and their relative abundance. One of the most commonly used fluorescent DNA dyes in immunocytochemistry applications is 4',6-diamidino-2-phenylindole dihydrochloride, known as DAPI. DAPI binds strongly to DNA and is used extensively for visualizing cell nuclei. It is excited by UV light and emits characteristic blue fluorescence. Here, we report a phenomenon based on an apparent photoconversion of DAPI that results in detection of a DAPI signal using a standard filter set for detection of green emission due to blue excitation. When a sample stained with DAPI only was first imaged with the green filter set (FITC/GFP), only a weak cytoplasmic autofluorescence was observed. Next, we imaged the sample with a DAPI filter set, obtaining a strong nuclear DAPI signal as expected. Upon reimaging the same samples with a FITC/GFP filter set, robust nuclear fluorescence was observed. We conclude that excitation with UV results in a photoconversion of DAPI that leads to detection of DAPI due to excitation and emission in the FITC/GFP channel. This phenomenon can affect data interpretation and lead to false-positive results when used together with fluorochrome-labeled nuclear proteins detected with blue excitation and green emission. In order to avoid misinterpretations, extra precaution should be taken to prepare staining solutions with low DAPI concentration and DAPI (UV excitation) images should be acquired after all other higher wavelength images. Of various DNA dyes tested, Hoechst 33342 exhibited the lowest photoconversion while that for DAPI and Hoechst 33258 was much stronger. Different fixation methods did not substantially affect the strength of photoconversion. We also suggest avoiding the use of mounting medium with high glycerol concentrations since glycerol showed the strongest impact on photoconversion. This photoconversion effect cannot be avoided even when using narrow bandpass filter sets.
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Zuo X, Djordjevic JT, Bijosono Oei J, Desmarini D, Schibeci SD, Jolliffe KA, Sorrell TC. Miltefosine induces apoptosis-like cell death in yeast via Cox9p in cytochrome c oxidase. Mol Pharmacol 2011; 80:476-85. [PMID: 21610197 DOI: 10.1124/mol.111.072322] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Miltefosine has antifungal properties and potential for development as a therapeutic for invasive fungal infections. However, its mode of action in fungi is poorly understood. We demonstrate that miltefosine is rapidly incorporated into yeast, where it penetrates the mitochondrial inner membrane, disrupting mitochondrial membrane potential and leading to an apoptosis-like cell death. COX9, which encodes subunit VIIa of the cytochrome c oxidase (COX) complex in the electron transport chain of the mitochondrial membrane, was identified as a potential target of miltefosine from a genomic library screen of the model yeast Saccharomyces cerevisiae. When overexpressed in S. cerevisiae, COX9, but not COX7 or COX8, led to a miltefosine-resistant phenotype. The effect of miltefosine on COX activity was assessed in cells expressing different levels of COX9. Miltefosine inhibited COX activity in a dose-dependent manner in Cox9p-positive cells. This inhibition most likely contributed to the miltefosine-induced apoptosis-like cell death.
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Affiliation(s)
- Xiaoming Zuo
- Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute and Sydney Emerging Infections and Biosecurity Institute, University of Sydney, Australia
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Biczók L, Wintgens V, Miskolczy Z, Megyesi M. Fluorescence Response of Alkaloids and DAPI on Inclusion in Cucurbit[7]uril: Utilization for the Study of the Encapsulation of Ionic Liquid Cations. Isr J Chem 2011. [DOI: 10.1002/ijch.201100027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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49
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Zhu Z, Xu L, Zhou X, Qin J, Yang C. Designing label-free DNA sequences to achieve controllable turn-off/on fluorescence response for Hg2+ detection. Chem Commun (Camb) 2011; 47:8010-2. [DOI: 10.1039/c1cc12384j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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50
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Senda N, Momotake A, Arai T. Fluorescence Enhancement in 7-Hydroxyquinoline Analogs by Methyl Substitution and Their Spectroscopic Characteristics in Aqueous Solution. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20100119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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