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Issar U, Arora R, Kakkar R. In silico studies of the interaction of the minor groove binder Hoechst 33258 with B-DNA. J Biomol Struct Dyn 2024; 42:4537-4552. [PMID: 37301606 DOI: 10.1080/07391102.2023.2220807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Interaction of the minor groove binder, Hoechst 33258, with the Dickerson-Drew DNA dodecamer sequence has been investigated using docking, MM/QM, MM/GBSA and molecular dynamics computations to study the modes of binding and the interactions responsible for the binding. Besides the original Hoechst 33258 ligand (HT), a total of 12 ionization and stereochemical states for the ligand are obtained at the physiological pH and have been docked into B-DNA. These states have one or the other or both benzimidazole rings in protonated states, apart from the piperazine nitrogen, which has a quaternary nitrogen in all the states. Most of these states are found to exhibit good docking scores and free energy of binding with B-DNA. The best docked state has been taken further for molecular dynamics simulations and compared with the original HT. This state is protonated at both benzimidazole rings besides the piperazine ring and hence has very highly negative coulombic interaction energy. In both cases, there are strong coulombic interactions, but these are offset by the almost equally unfavorable solvation energies. Thus, the nonpolar forces, particularly van der Waals contacts, dominate the interaction, and the polar interactions highlight subtle changes in the binding energies, leading to more highly protonated states having more negative binding energies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Upasana Issar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Kalindi College, University of Delhi, Delhi, India
| | - Richa Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Shivaji College, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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Singh Chauhan S, Mohan Murari B. Fluorescence Spectroscopic Studies to Evaluate Binding Interaction between Hoechst 33258 and Bilirubin. J Fluoresc 2023:10.1007/s10895-023-03440-8. [PMID: 37728846 DOI: 10.1007/s10895-023-03440-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
A detailed spectroscopic study (fluorescence, absorption, and lifetime) was conducted to gain insight into the nature of the binding interaction between fluorophore Hoechst33258 (H258) and jaundice marker Bilirubin (Br). The fluorescence emission of the H258 (Ex/Em = 340-502nm) showed a conc. dependent quenching in the presence of Br (1.25[Formula: see text]M to 10[Formula: see text]M). The Stern-Volmer constant demonstrated an upward curve depicting the occurrence of both static and dynamic quenching with an acquired value of K[Formula: see text] = 3.1x 10[Formula: see text] M[Formula: see text] and biomolecular quenching rate constant K[Formula: see text] = 8.6 x 10[Formula: see text] M[Formula: see text]S[Formula: see text]. The static quenching was evaluated using the sphere of action model and a sphere radius of 0.3nm indicated the presence of a static component in the quenching. The FRET analysis with overlap integral (J) = 1.4x10[Formula: see text] M[Formula: see text]cm[Formula: see text]nm[Formula: see text] and Foster Radius(R[Formula: see text]) = 26.82 Å with 59% efficiency suggested occurrence of dynamic quenching. Further studies with the time-resolved fluorescence also indicated the presence of dynamic quenching. The lifetime values of H258 reduced from 3.9ns to 0.5ns. Molecular docking studies further support both static and dynamic components in quenching. A non-covalent interaction of H258 with Br in the presence of HSA is predominantly characterized by H-bonding with residues Lys, Asn, Glu, Gln, and Br. The H258 and Br interaction was within the distance of 3.04 Å, which is in coherence with the sphere of action model (0.3nm) and Van-der-Waals along with hydrophobic interactions, which suggested both static and dynamic quenching. Thus, H258 can serve as an efficient fluorophore to monitor binding interactions and can be further exploited as a suitable probe for investigating conformational changes and detection of Br in subsequent studies.
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Affiliation(s)
- Srishti Singh Chauhan
- Department of Sensor and Biomedical Technology, School of Electronics Engineering, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Bhaskar Mohan Murari
- Department of Sensor and Biomedical Technology, School of Electronics Engineering, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
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Morozov VN, Klimovich MA, Shibaeva AV, Klimovich ON, Koshevaya ED, Kolyvanova MA, Kuzmin VA. Optical Polymorphism of Liquid-Crystalline Dispersions of DNA at High Concentrations of Crowding Polymer. Int J Mol Sci 2023; 24:11365. [PMID: 37511123 PMCID: PMC10379083 DOI: 10.3390/ijms241411365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Optically active liquid-crystalline dispersions (LCD) of nucleic acids, obtained by polymer- and salt-induced (psi-) condensation, e.g., by mixing of aqueous saline solutions of low molecular weight DNA (≤106 Da) and polyethylene glycol (PEG), possess an outstanding circular dichroism (CD) signal (so-called psi-CD) and are of interest for sensor applications. Typically, such CD signals are observed in PEG content from ≈12.5% to ≈22%. However, in the literature, there are very conflicting data on the existence of psi-CD in DNA LCDs at a higher content of crowding polymer up to 30-40%. In the present work, we demonstrate that, in the range of PEG content in the system above ≈24%, optically polymorphic LCDs can be formed, characterized by both negative and positive psi-CD signals, as well as by ones rather slightly differing from the spectrum of isotropic DNA solution. Such a change in the CD signal is determined by the concentration of the stock solution of PEG used for the preparation of LCDs. We assume that various saturation of polymer chains with water molecules may affect the amount of active water, which in turn leads to a change in the hydration of DNA molecules and their transition from B-form to Z-form.
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Affiliation(s)
- Vladimir N Morozov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Mikhail A Klimovich
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Anna V Shibaeva
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Olga N Klimovich
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Ekaterina D Koshevaya
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Maria A Kolyvanova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Vladimir A Kuzmin
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
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Cooksey CJ. Abbreviations for dyes, stains and fluorescent probes used in biology and medicine in the 21st century. A bright future or the last gasp? Biotech Histochem 2021; 96:401-407. [PMID: 33745408 DOI: 10.1080/10520295.2021.1897677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
I summarize here the history of the use of abbreviations, mostly in subject areas related to dyes, stains and fluorescent probes used in biology and medicine. The dozen most popular abbreviations in these fields are identified and their salient characteristics noted. The pros and cons of each abbreviation are discussed with relevant citations. Certain abbreviations that are not in the list, e.g., AZAN and LN, are mentioned because they have an unusual origin; while others, i.e., INEPT and INADEQUATE are presented because they are bizarre. A related topic is abbreviations used for citations, which require further efforts to decipher. In the past, brevity helped conserve materials, such as ink and paper, and promoted more rapid publishing. I suggest that the use of many abbreviations in the current era of electronic publishing may not be necessary.
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Flauzino JMR, Peres RCS, Alves LM, Vieira JG, Dos Santos JG, Brito-Madurro AG, Madurro JM. DNA electrochemical biosensor for detection of Alicyclobacillus acidoterrestris utilizing Hoechst 33258 as indicator. Bioelectrochemistry 2021; 140:107801. [PMID: 33789176 DOI: 10.1016/j.bioelechem.2021.107801] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/10/2021] [Accepted: 03/14/2021] [Indexed: 01/18/2023]
Abstract
Alicyclobacillus acidoterrestris is an acidophilic and thermophilic bacterium present in the soil, often associated with the spoilage of acidic juices, such as orange juice. Their spores resist pasteurization and, when reactivated, modify the organoleptic properties of the juice, making it unsuitable for consumption, due mainly to production of guaiacol. Biosensors are detection devices that respond quickly and are easy to handle, with great potential for use in the juice production chain. In this context, this work reports an electrochemical genosensor for detection of A. acidoterrestris, based on a graphite electrode modified with electrochemically reduced graphene oxide, a polymer derived from 3-hydroxybenzoic acid and a specific DNA probe sequence complementary with the genomic DNA of A. acidoterrestris. Detection of the target was performed by monitoring the oxidation peak of the Hoechst 33258, a common DNA stainer. The genosensor detection limit was 12 ng mL-1 and it kept 77% of response after ten weeks, and a test showed that orange juice does not interfere with bacteria lysate detection. This biosensor is the first platform for electrochemical detection of the genomic DNA of A. acidoterrestris in the literature, and the first to use Hoechst 33258 as indicator with whole genomic DNA molecules.
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Affiliation(s)
- José M R Flauzino
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, Brazil.
| | - Rafaela C S Peres
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Lívia M Alves
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Jussara G Vieira
- Institute of Chemistry, Federal University of Uberlandia, Uberlandia, Brazil
| | - Júlia G Dos Santos
- Faculty of Chemistry Engineering, Federal University of Uberlândia, Uberlandia, Brazil
| | - Ana G Brito-Madurro
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, Brazil
| | - João M Madurro
- Institute of Chemistry, Federal University of Uberlandia, Uberlandia, Brazil
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Amirbekyan KY, Shahinyan GA, Ghazoyan HH, Sargsyan HR, Markarian SA. Fluorescence anisotropy studies on the Hoechst 33258-DNA interaction: the solvent effect. J Biomol Struct Dyn 2020; 39:4902-4906. [PMID: 32568619 DOI: 10.1080/07391102.2020.1782267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Fluorescence anisotropy method was applied to characterize the interactions of DNA minor groove binder Hoechst 33258 with different solvents without and in the presence of DNA. It is important to study the interaction of small molecules with DNA for the purpose of better understanding the mechanism of their action, as well as to design novel and more effective compounds. Spectroscopic study of the ligand in different binary mixed solvents containing DMSO, alcohols and buffer was carried out. Studies were performed without and in the presence of DNA. Fluorescence anisotropy studies reveal the characteristics of Hoechst 33258 in different mixed solvents. The results show the strong dependence of the anisotropy of Hoechst 33258 on solvent content, viscosity and intermolecular interactions. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karen Yu Amirbekyan
- Department of Physical Chemistry, Yerevan State University, Yerevan, Armenia
| | - Gohar A Shahinyan
- Department of Physical Chemistry, Yerevan State University, Yerevan, Armenia
| | - Heghine H Ghazoyan
- Department of Physical Chemistry, Yerevan State University, Yerevan, Armenia
| | - Hasmik R Sargsyan
- Department of Physical Chemistry, Yerevan State University, Yerevan, Armenia
| | - Shiraz A Markarian
- Department of Physical Chemistry, Yerevan State University, Yerevan, Armenia
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Carter MLJ, Rusling DA, Gurr S, Brown T, Fox KR. Stability of the different arms of a DNA tetrahedron and its interaction with a minor groove ligand. Biophys Chem 2019; 256:106270. [PMID: 31706136 DOI: 10.1016/j.bpc.2019.106270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/02/2019] [Accepted: 10/02/2019] [Indexed: 11/27/2022]
Abstract
DNA strands can be designed to assemble into stable three-dimensional structures, based on Watson-Crick base pairing rules. The simplest of these is the DNA tetrahedron that is composed of four oligonucleotides. We have re-designed the sequence of a DNA tetrahedron so that it contains a single (AATT) binding site for the minor groove binding ligand Hoechst 33258. We examined the stability of this structure by placing fluorescent groups within each of its edges and have shown that all the edges melt at the same temperature in the absence of the ligand. The minor groove ligand still binds to its recognition sequence within the tetrahedron and increases the melting temperature of the folded complex. This ligand-induced stabilisation is propagated into the adjacent helical arms and the tetrahedron melts as a single entity in a cooperative fashion.
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Affiliation(s)
- Michael L J Carter
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - David A Rusling
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Steven Gurr
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Keith R Fox
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom.
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Forson PO, Tetteh-Quarcoo PB, Ahenkorah J, Aryee R, Okine EN, Afutu E, Djameh GI, Agyapong J, Anang AK, Ayeh-Kumi PF. Ability of Vital and Fluorescent Staining in the Differentiation of Schistosoma haematobium Live and Dead Eggs. Med Sci (Basel) 2019; 7:medsci7040064. [PMID: 31018598 PMCID: PMC6524036 DOI: 10.3390/medsci7040064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 03/21/2019] [Accepted: 04/10/2019] [Indexed: 11/16/2022] Open
Abstract
This study reports (for the first time) the staining ability of vital (0.4% trypan blue and 1% neutral red) and fluorescent (Hoechst 33258) dyes to differentiate between live and dead Schistosoma haematobium (S. haematobium) eggs in human urine samples. Since S. haematobium egg is important in disease pathology, diagnosis, transmission, and drug development research, it is essential to be able to easily distinguish live eggs from dead ones. Staining is considered a way of enhancing the identification of live and dead eggs. Urine samples from school children were examined for the presence of S. haematobium eggs. Vital and fluorescent dyes were used to stain the samples that contained S. haematobium eggs, after which they were observed using light and fluorescent microscopes, respectively. The Hoechst 33258 provided a good staining outcome for differentiation between live and dead eggs, followed by 0.4% Trypan blue. Regarding the 1% neutral red stain, even though it provided some evidence of which egg was alive or dead, the distinction was not very clear; therefore, it could be useful when used in combination with other stains for egg viability determination. The benefits of this study will include assessing the effect of drugs on S. haematobium eggs in Schistosomiasis research.
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Affiliation(s)
- Peter O Forson
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - Patience B Tetteh-Quarcoo
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - John Ahenkorah
- Department of Anatomy, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - Robert Aryee
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 233, Ghana.
- Department of Physiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - Esther N Okine
- Central Laboratory Services, Korle-Bu Teaching Hospital, Korle-Bu, Accra 233, Ghana.
| | - Emmanuel Afutu
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - Georgina I Djameh
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - Jeffrey Agyapong
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - Abraham K Anang
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra 233, Ghana.
| | - Patrick F Ayeh-Kumi
- Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra 233, Ghana.
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Vekshin NL, Doynikova AN, Lvov AM. Determination of Micro-Quantities of DNA Using DNAse and Fluorescence of Hoechst 33258 and Light-Scattering. J Fluoresc 2019; 29:479-484. [PMID: 30811018 DOI: 10.1007/s10895-019-02358-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
The DNA hydrolysis by deoxyribonuclease (DNAse I) in aqueous solution was studied, using fluorescence spectroscopy and high-sensitive light-scattering detection. Specific hydrolysis of high-polymer DNA or fragmented DNA by the enzyme led to a strong decrease in the fluorescence of the Hoechst dye. The hydrolysis of mitochondrial DNA was accompanied by a decrease in the fluorescence of the dye only in 1.6 times. Hydrolysis within minutes and even hours led to appearance of large polynucleotide fragments, but not to short oligonucleotides, that was confirmed using polarized fluorescence and highly sensitive measurement of light-scattering. At the moment of the time of formation of a complex between DNA and DNAse I, a strong light-scattering occurred, which then dropped sharply during hydrolysis of high-molecular DNA, and slowly decreased during hydrolysis of fragmented DNA. The proposed methods can be applied for selective detection of trace amounts of various types of DNA, as well as for studying their physic-chemical properties.
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Affiliation(s)
- N L Vekshin
- Institute of Cell Biophysics of PSC of RAS, Pushchino, Moscow Region, Russian Federation, 142290
| | - A N Doynikova
- Institute of Cell Biophysics of PSC of RAS, Pushchino, Moscow Region, Russian Federation, 142290. .,Kazan (Volga Region) Federal University, Kazan, Russian Federation.
| | - A M Lvov
- Institute of Cell Biophysics of PSC of RAS, Pushchino, Moscow Region, Russian Federation, 142290
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Beggiato S, Borelli AC, Ferraro L, Tanganelli S, Antonelli T, Tomasini MC. Palmitoylethanolamide Blunts Amyloid-β42-Induced Astrocyte Activation and Improves Neuronal Survival in Primary Mouse Cortical Astrocyte-Neuron Co-Cultures. J Alzheimers Dis 2018; 61:389-399. [PMID: 29154284 DOI: 10.3233/jad-170699] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Based on the pivotal role of astrocytes in brain homeostasis and the strong metabolic cooperation existing between neurons and astrocytes, it has been suggested that astrocytic dysfunctions might cause and/or contribute to neuroinflammation and neurodegenerative processes. Therapeutic approaches aimed at both neuroprotection and neuroinflammation reduction may prove particularly effective in slowing the progression of these diseases. The endogenous lipid mediator palmitoylethanolamide (PEA) displayed neuroprotective and anti(neuro)inflammatory properties, and demonstrated interesting potential as a novel treatment for Alzheimer's disease. OBJECTIVE AND METHODS We firstly evaluated whether astrocytes could participate in regulating the Aβ42-induced neuronal damage, by using primary mouse astrocytes cell cultures and mixed astrocytes-neurons cultures. Furthermore, the possible protective effects of PEA against Aβ42-induced neuronal toxicity have also been investigated by evaluating neuronal viability, apoptosis, and morphometric parameters. RESULTS The presence of astrocytes pre-exposed to Aβ42 (0.5μM; 24 h) induced a reduction of neuronal viability in primary mouse astrocytes-neurons co-cultures. Furthermore, under these experimental conditions, an increase in the number of neuronal apoptotic nuclei and a decrease in the number of MAP-2 positive neurons were observed. Finally, astrocytic Aβ42 pre-exposure induced an increase in the number of neurite aggregations/100μm as compared to control (i.e., untreated) astrocytes-neurons co-cultures. These effects were not observed in neurons cultured in the presence of astrocytes pre-exposed to PEA (0.1μM), applied 1 h before and maintained during Aβ42 treatment. CONCLUSION Astrocytes contribute to Aβ42-induced neurotoxicity and PEA, by blunting Aβ42-induced astrocyte activation, improved neuronal survival in mouse astrocyte-neuron co-cultures.
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Affiliation(s)
- Sarah Beggiato
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy.,IRET Foundation, Ozzano Emilia, Bologna, Italy
| | | | - Luca Ferraro
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy.,IRET Foundation, Ozzano Emilia, Bologna, Italy.,LTTA Centre, University of Ferrara, Italy
| | - Sergio Tanganelli
- IRET Foundation, Ozzano Emilia, Bologna, Italy.,Department of Medical Sciences, University of Ferrara, Italy.,LTTA Centre, University of Ferrara, Italy
| | - Tiziana Antonelli
- IRET Foundation, Ozzano Emilia, Bologna, Italy.,Department of Medical Sciences, University of Ferrara, Italy.,LTTA Centre, University of Ferrara, Italy
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11
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Bhaduri S, Ranjan N, Arya DP. An overview of recent advances in duplex DNA recognition by small molecules. Beilstein J Org Chem 2018; 14:1051-1086. [PMID: 29977379 PMCID: PMC6009268 DOI: 10.3762/bjoc.14.93] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.
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Affiliation(s)
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research (NIPER), Raebareli 122003, India
| | - Dev P Arya
- NUBAD, LLC, 900B West Faris Rd., Greenville 29605, SC, USA.,Clemson University, Hunter Laboratory, Clemson 29634, SC, USA
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12
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Bhavani G, Sivaprakash S, Samuel CR, Santhiya ST. Enhanced Expression of FRA16B using AT-Rich DNA Binding Chemicals in a Woman with Secondary Amenorrhoea. J Clin Diagn Res 2017; 11:QD01-QD03. [PMID: 28764253 DOI: 10.7860/jcdr/2017/26545.10043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/25/2017] [Indexed: 11/24/2022]
Abstract
Fragile sites represent regions of chromatin that fail to compact during mitosis. Based on the prevalence and pattern of inheritance they are classified as rare fragile sites or common fragile sites. Rare fragile sites either occur spontaneously or can be induced by certain AT-specific binding chemicals namely distamycin, Hoechst 33258, Berenil and others. The most common of all rare autosomal fragile sites is fra(16)(q22) with a heterozygote frequency of ~5%. FRA16B results from an expansion of a 33 bp AT-rich Minisatellite repeat. These rare forms are usually heritable and segregate in a Mendelian fashion. The proband who was referred for secondary amenorrhoea, revealed 46,XX,fra(16)(q22.1)pat karyotype. Her father and younger sibling were also found to be carriers. This study aimed to delineate the genotypic and phenotypic features exhibited by these carriers and to evaluate FRA16B expression using AT-specific binding chemicals. The additives employed were Berenil, BrdU and Hoechst 33258. Berenil at a concentration of 150 µg/ml showed the highest expression of FRA16B. Although the recent breakthrough in molecular characterization of fragile sites plays a critical role in comprehending their association with various diseases, the physiological link between them and amenorrhoea is not clearly understood.
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Affiliation(s)
- Gunasekaran Bhavani
- Ph.D. Research Scholar, Department of of Genetics, Dr. ALM Postgraduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, Tamil Nadu, India
| | - S Sivaprakash
- Assistant Professor, Department of Endocrinology and Diabetology, Institute of Obstetrics and Gynaecology, Government Hospital for Women and Children, Egmore, Chennai, Tamil Nadu, India
| | - Chandra R Samuel
- Associate Professor, Department of of Genetics, Dr. ALM Postgraduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, Tamil Nadu, India
| | - Sathiyavedu Thyagarajan Santhiya
- Professor and Head (Retd.), Department of of Genetics, Dr. ALM Postgraduate Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, Tamil Nadu, India
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13
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Ranjan N, Arya DP. Linker dependent intercalation of bisbenzimidazole-aminosugars in an RNA duplex; selectivity in RNA vs. DNA binding. Bioorg Med Chem Lett 2016; 26:5989-5994. [PMID: 27884695 PMCID: PMC6201841 DOI: 10.1016/j.bmcl.2016.10.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023]
Abstract
Neomycin and Hoechst 33258 are two well-known nucleic acid binders that interact with RNA and DNA duplexes with high affinities respectively. In this manuscript, we report that covalent attachment of bisbenzimidazole unit derived from Hoechst 33258 to neomycin leads to intercalative binding of the bisbenzimidazole unit (oriented at 64-74° with respected to the RNA helical axis) in a linker length dependent manner. The dual binding and intercalation of conjugates were supported by thermal denaturation, CD, LD and UV-Vis absorption experiments. These studies highlight the importance of linker length in dual recognition by conjugates, for effective RNA recognition, which can lead to novel ways of recognizing RNA structures. Additionally, the ligand library screens also identify DNA and RNA selective compounds, with compound 9, containing a long linker, showing a 20.3°C change in RNA duplex Tm with only a 13.0°C change in Tm for the corresponding DNA duplex. Significantly, the shorter linker in compound 3 shows almost the reverse trend, a 23.8°C change in DNA Tm, with only a 9.1°C change in Tm for the corresponding RNA duplex.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States
| | - Dev P Arya
- Laboratory of Bioorganic and Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States.
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Chandrika NT, Shrestha SK, Ngo HX, Garneau-Tsodikova S. Synthesis and investigation of novel benzimidazole derivatives as antifungal agents. Bioorg Med Chem 2016; 24:3680-6. [PMID: 27301676 DOI: 10.1016/j.bmc.2016.06.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 01/02/2023]
Abstract
The rise and emergence of resistance to antifungal drugs by diverse pathogenic fungal strains have resulted in an increase in demand for new antifungal agents. Various heterocyclic scaffolds with different mechanisms of action against fungi have been investigated in the past. Herein, we report the synthesis and antifungal activities of 18 alkylated mono-, bis-, and trisbenzimidazole derivatives, their toxicities against mammalian cells, as well as their ability to induce reactive oxygen species (ROS) in yeast cells. Many of our bisbenzimidazole compounds exhibited moderate to excellent antifungal activities against all tested fungal strains, with MIC values ranging from 15.6 to 0.975μg/mL. The fungal activity profiles of our bisbenzimidazoles were found to be dependent on alkyl chain length. Our most potent compounds were found to display equal or superior antifungal activity when compared to the currently used agents amphotericin B, fluconazole, itraconazole, posaconazole, and voriconazole against many of the strains tested.
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15
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Satam V, Babu B, Patil P, Brien KA, Olson K, Savagian M, Lee M, Mepham A, Jobe LB, Bingham JP, Pett L, Wang S, Ferrara M, Bruce CD, Wilson WD, Lee M, Hartley JA, Kiakos K. AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide. Bioorg Med Chem Lett 2015; 25:3681-5. [PMID: 26122210 DOI: 10.1016/j.bmcl.2015.06.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 11/30/2022]
Abstract
The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx, 2-(p-anisyl)-4-aza-benzimidazole-5-carboxamide, is a novel, fluorescent DNA recognition element, derived from Hoechst 33258 to recognize G·C base pairs. Supported by theoretical data, the results from DNase I footprinting, CD, ΔT(M), and SPR studies provided evidence that an azaHx/IP pairing, formed from antiparallel stacking of two azaHx-PI molecules in a side-by-side manner in the minor groove, selectively recognized a C-G doublet. AzaHx-PI was found to target 5'-ACGCGT-3', the Mlu1 Cell Cycle Box (MCB) promoter sequence with specificity and significant affinity (K(eq) 4.0±0.2×10(7) M(-1)).
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Affiliation(s)
- Vijay Satam
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Balaji Babu
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Pravin Patil
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kimberly A Brien
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kevin Olson
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Mia Savagian
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Megan Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Andrew Mepham
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Laura Beth Jobe
- Department of Chemistry, Erskine College, Due West, SC 29639, United States
| | - John P Bingham
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Luke Pett
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Maddi Ferrara
- Department of Chemistry, John Carroll University, University Heights, OH 44118, United States
| | - Chrystal D Bruce
- Department of Chemistry, John Carroll University, University Heights, OH 44118, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Moses Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States; Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States.
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
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16
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Bukhari M, Deng H, Jones N, Towne Z, Woodworth CD, Samways DSK. Selective permeabilization of cervical cancer cells to an ionic DNA-binding cytotoxin by activation of P2Y receptors. FEBS Lett 2015; 589:1498-504. [PMID: 25937122 PMCID: PMC4497545 DOI: 10.1016/j.febslet.2015.04.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/20/2015] [Indexed: 10/23/2022]
Abstract
Extracellular ATP is known to permeabilize certain cell types to polyatomic cations like YO-PRO1. Here, we report that extracellularly applied ATP stimulated rapid uptake and accumulation of an otherwise weakly membrane permeable fluorescent DNA-binding cytotoxin, Hoechst 33258, into cervical cancer cells. While ATP stimulated Hoechst 33258 uptake in 20-70% of cells from seven cervical cancer cell lines, it stimulated uptake in less than 8% of cervical epithelial cells obtained from the normal transformation zone and ectocervix tissue of 11 patients. ATP-evoked Hoechst 33258 uptake was independent of ionotropic P2X receptors, but dependent on activation of P2Y receptors. Thus, we show here that cervical cancer cells can be selectively induced to take up and accumulate an ionic cytotoxin by exposure to extracellular ATP.
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Affiliation(s)
- Maurish Bukhari
- Department of Biology, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699-5805, USA
| | - Han Deng
- Department of Biology, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699-5805, USA
| | - Noelle Jones
- Department of Biology, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699-5805, USA
| | - Zachary Towne
- Department of Biology, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699-5805, USA
| | - Craig D Woodworth
- Department of Biology, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699-5805, USA
| | - Damien S K Samways
- Department of Biology, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699-5805, USA.
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Shahabadi N, Bagheri S. Spectroscopic and molecular docking studies on the interaction of the drug olanzapine with calf thymus DNA. Spectrochim Acta A Mol Biomol Spectrosc 2015; 136 Pt C:1454-1459. [PMID: 25459706 DOI: 10.1016/j.saa.2014.10.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/22/2014] [Accepted: 10/13/2014] [Indexed: 06/04/2023]
Abstract
The present study investigated the binding interaction between olanzapine and calf thymus DNA (ct-DNA) using emission, absorption, circular dichroism, viscosity measurements and molecular modeling. Thermodynamic parameters (ΔH<0 and ΔS<0) indicated that hydrogen bond and van der Waals play main roles in the binding of the drug to ct-DNA. Spectrophotometric studies of the interaction of olanzapine with DNA have shown that it could bind to ct-DNA (Kb=2×10(3)M(-1)). The binding constant is comparable to standard groove binding drugs. Competitive fluorimetric studies with Hoechst 33258 have shown that olanzapine exhibits the ability to displace the DNA-bound Hoechst 33258 indicating that binds strongly in minor groove of DNA helix. Furthermore, the drug induces detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity. All of the experimental results prove that the groove binding must be predominant. The results obtained from experimental data were in good agreement with molecular modeling studies.
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Affiliation(s)
- Nahid Shahabadi
- Department of Chemistry, Faculty of Science, Razi University, Kermanshah, Iran.
| | - Somayeh Bagheri
- Department of Chemistry, Faculty of Science, Razi University, Kermanshah, Iran
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