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Pansare AV, Shedge AA, Sonawale MC, Pansare SV, Mahakal AD, Khairkar SR, Chhatre SY, Kulal DK, Patil VR. Deciphering the sensing of α-amyrin acetate with hs-DNA: a multipronged biological probe. RSC Adv 2022; 12:1238-1243. [PMID: 35425164 PMCID: PMC8978960 DOI: 10.1039/d1ra07195e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/15/2021] [Indexed: 11/22/2022] Open
Abstract
In this study, we focus on the biomimetic development of small molecules and their biological sensing with DNA. The binding of herring sperm deoxyribonucleic acid (hs-DNA) with naturally occurring bioactive small molecule α-amyrin acetate (α-AA), a biomimetic - isolated from the leaves of Ficus (F.) arnottiana is investigated. Collective information from various imaging, spectroscopic and biophysical experiments provides evidence that α-AA is a minor groove sensor of hs-DNA and preferentially binds to the A-T-rich regions. Interactions of different concentrations of small molecule α-AA with hsDNA were evaluated via various analytical techniques such as UV-Vis, circular dichroism (CD) and fluorescence emission spectroscopy. Fluorescence emission spectroscopy results suggest that α-AA decreases the emission level of hsDNA. DNA minor groove sensor Hoechst 33258 and intercalative sensor EB, melting transition analysis (T M) and viscosity analysis clarified that α-AA binds to hs-DNA via a groove site. Biophysical chemistry and molecular docking studies show that hydrophobic interactions play a major role in this binding. The present research deals with a natural product biosynthesis-linked chemical-biology interface sensor as a biological probe for α-AA: hs-DNA.
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Affiliation(s)
- Amol V Pansare
- Composite Group, Swiss Federal Laboratories for Materials Science and Technology-Empa 8600 Dübendorf Switzerland
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Amol A Shedge
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | | | - Shubham V Pansare
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Akshay D Mahakal
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Shyam R Khairkar
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Shraddha Y Chhatre
- National Chemical Laboratory (NCL) Dr. Homi Bhabha Road Pune 411008 India
| | - Dnyaneshwar K Kulal
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Vishwanath R Patil
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
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Banerjee A, Majumder P, Sanyal S, Singh J, Jana K, Das C, Dasgupta D. The DNA intercalators ethidium bromide and propidium iodide also bind to core histones. FEBS Open Bio 2014; 4:251-9. [PMID: 24649406 PMCID: PMC3958746 DOI: 10.1016/j.fob.2014.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 01/17/2023] Open
Abstract
Eukaryotic DNA is compacted in the form of chromatin, in a complex with histones and other non-histone proteins. The intimate association of DNA and histones in chromatin raises the possibility that DNA-interactive small molecules may bind to chromatin-associated proteins such as histones. Employing biophysical and biochemical techniques we have characterized the interaction of a classical intercalator, ethidium bromide (EB) and its structural analogue propidium iodide (PI) with hierarchical genomic components: long chromatin, chromatosome, core octamer and chromosomal DNA. Our studies show that EB and PI affect both chromatin structure and function, inducing chromatin compaction and disruption of the integrity of the chromatosome. Calorimetric studies and fluorescence measurements of the ligands demonstrated and characterized the association of these ligands with core histones and the intact octamer in absence of DNA. The ligands affect acetylation of histone H3 at lysine 9 and acetylation of histone H4 at lysine 5 and lysine 8 ex vivo. PI alters the post-translational modifications to a greater extent than EB. This is the first report showing the dual binding (chromosomal DNA and core histones) property of a classical intercalator, EB, and its longer analogue, PI, in the context of chromatin.
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Affiliation(s)
- Amrita Banerjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Parijat Majumder
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Sulagna Sanyal
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Jasdeep Singh
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Kuladip Jana
- Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
| | - Chandrima Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Dipak Dasgupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
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3
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Abstract
We have studied intercalation of ethidium bromide (EB) to genomic DNA encapsulated in a nanospace of an anionic AOT reverse micelle (RM). Circular dichroism (CD) study on the DNA in the RM reveals its condensed form. Here, we have used temporal decay-associated spectra (DAS) and time-resolved area normalized emission spectral (TRANES) techniques to investigate EB-binding to condensed DNA because the interference of emission from unbound EB in the RM makes conventional steady state and picosecond resolved fluorescence spectroscopic techniques challenging. The binding affinity of the ligand EB with the DNA in the RM is found to increase with the size of the RM, reflecting the effect of lessening of DNA condensation on the binding affinity. CD spectra of the DNA in the RM with various sizes indicate the structural change of the condensed DNA with reverse micellar size. DAS and TRANES techniques along with dynamic light scattering studies of the EB-DNA complex in the RM further reveal two kinds of binding modes of the ligand with the condensed DNA even in essentially monodispersed RMs. To investigate the role of RM on the ligand binding and secondary structure of the DNA, we have also studied complexation of EB with two synthetic self-complimentary oligonucleotides of sequences (CGCAAATTTGCG)2 and (CGCGCGCGCGCG)2 in the RM.
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Affiliation(s)
- Rupa Sarkar
- Department of Chemical, Biological and Macromolecular Sciences, Unit for Nano Science and Technology, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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Pal SK, Mandal D, Bhattacharyya K. Photophysical Processes of Ethidium Bromide in Micelles and Reverse Micelles. J Phys Chem B 1998. [DOI: 10.1021/jp982126c] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Samir Kumar Pal
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India
| | - Debabrata Mandal
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India
| | - Kankan Bhattacharyya
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India
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Bertuzzi A, D'Agnano I, Gandolfi A, Graziano A, Starace G, Ubezio P. Study of propidium iodide binding to DNA in intact cells by flow cytometry. CELL BIOPHYSICS 1990; 17:257-67. [PMID: 1714351 DOI: 10.1007/bf02990721] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We studied the in situ binding of propidium iodide to DNA in fixed human lymphocytes, using flow cytometry. Experimental data of fluorescence emission vs dye concentration and vs cell concentration were obtained. Data were interpreted by means of two different mathematical models specific for the staining reaction, and the binding parameters were obtained by "best-fitting" of the data. A model based on two classes of binding sites with different affinity constants gave the most satisfactory fitting. The accessibility of the in situ chromatin turned out to be reduced with respect to the non in situ accessibility for ethidium bromide as reported in the literature. The present study shows the usefulness of the flow-cytometric technique for probing DNA structure in intact cells.
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Affiliation(s)
- A Bertuzzi
- Istituto di Analisi dei Sistemi ed Informatica del CNR, Viale Manzoni, Roma, Italy
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Cuniberti C, Guenza M. Environment-induced changes in DNA conformation as probed by ethidium bromide fluorescence. Biophys Chem 1990; 38:11-22. [PMID: 2085645 DOI: 10.1016/0301-4622(90)80035-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The interaction of the ethidium cation with calf thymus DNA is investigated in solutions of different ionic strength and temperature by observation of the enhancement of fluorescence of ethidium upon intercalation in the duplex structure. The quantum yield of the fluorescence of the intercalated dye is found to increase either upon lowering the Na+ concentration or upon increasing the temperature. The existence of a correlation between the geometry of the intercalation complex and the features of the secondary structure of DNA is suggested. Binding isotherms under corresponding environmental conditions are also quantitated by fluorescence enhancement and interpreted in terms of the neighbor exclusion model. Large contributions from change in hydration to the thermodynamics of binding are demonstrated by the temperature dependences of the equilibrium constants. The neighbor exclusion range is found to be practically independent of the salt concentration but its value increases from an average of 2.4 around room temperature to 4-5 at 80 degrees C, as inferred from the binding curves in 0.15 and 0.5 M [Na+] or from the DNA hypochromism vs temperature profiles of complexes at 10(-3) M [Na+]. All the data point to a possible sequence-conformation specificity in the intercalation of ethidium which in heterogeneous DNA is mediated by environmental changes.
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Affiliation(s)
- C Cuniberti
- Istituto di Chimica Industriale, Università di Genova, Italy
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Giangarè MC, Prosperi E, Pedrali-Noy G, Bottiroli G. Flow cytometric evaluation of DNA stainability with propidium iodide after histone H1 extraction. CYTOMETRY 1989; 10:726-30. [PMID: 2582963 DOI: 10.1002/cyto.990100609] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A flow cytometric evaluation of the effect of the histone H1 extraction on DNA stainability with propidium iodide was performed on isolated HeLa nuclei. Selective removal of the lysine-rich protein was attained by using two established techniques involving treatment with 0.7 M NaCl or low pH. DNA stainability was monitored at different dye/DNA-P ratios, varying from low to high saturating concentrations. Depletion of the histone H1from nuclei results in the transition from low to high affinity of a portion of binding sites, as shown by 1) the increase in fluorescence intensity after staining with the dye at low saturating concentrations and 2) the higher value of the fluorescence intensity ratio (FI5/FI50) exhibited by H1-depleted nuclei stained with a low (5 micrograms/ml) vs. a high (50 micrograms/ml) concentration, as compared with control samples.
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Affiliation(s)
- M C Giangarè
- Centro di Studio per l'Istochimica del CNR, Dipartimento di Biologia Animale, Università di Pavia, Italy
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8
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Coffman GL, Yielding LW, Yielding L. Monoazido analog of ethidium as a chromatin probe: binding to DNA. Biopolymers 1984; 23:1067-84. [PMID: 6733248 DOI: 10.1002/bip.360230608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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McPherson DD, Pezzuto JM. Interaction of 9-aminoacridine, ethidium bromide and harman with DNA characterized by size exclusion high-performance liquid chromatography. J Chromatogr A 1983; 281:348-54. [PMID: 6668336 DOI: 10.1016/s0021-9673(01)87898-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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10
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Mantooth D, Georghiou S. Complex formation between ethidium bromide and the nucleotides AMP and GMP. Photochem Photobiol 1983; 38:623-6. [PMID: 6316377 DOI: 10.1111/j.1751-1097.1983.tb03393.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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11
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Mazzini G, Giordano P, Riccardi A, Montecucco CM. A flow cytometric study of the propidium iodide staining kinetics of human leukocytes and its relationship with chromatin structure. CYTOMETRY 1983; 3:443-8. [PMID: 6189681 DOI: 10.1002/cyto.990030610] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Schmitz KS. A model for the association of intercalating ligands with mononucleosomes and chromatin. J Theor Biol 1982; 98:29-43. [PMID: 7176667 DOI: 10.1016/0022-5193(82)90056-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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13
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Genest D, Wahl P, Erard M, Champagne M, Daune M. Fluorescence anisotropy decay of ethidium bromide bound to nucleosomal core particles. Biochimie 1982; 64:419-27. [PMID: 7115784 DOI: 10.1016/s0300-9084(82)80580-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We have measured the fluorescence anisotropy decay of ethidium bromide bound to nucleosomal core particles (145 DNA base pairs) for very small values of the binding ratio (0.0005 less than or equal to r less than or equal to 0.01). For r = 0.0005 the anisotropy decay could be described by a sum of two exponential functions. The two correlation times theta 1 and theta 2 increase with r until r congruent to 0.0025 and then decrease while the apparent fundamental anisotropy A'0 decreases until r congruent to 0.0025 and then remains constant. The anisotropy decay parameters of the first ethidium molecule bound to a core particle have been obtained by extrapolating theta 1, theta 2 and A'0 to r = 0. We propose the following interpretation of these results. The first bound ethidium molecule is located on a DNA segment linked by its two ends to the histone core. This ethidium molecule follows the torsional motion of the DNA segment. The length of this segment (15 base pairs) was determined by fitting a mathematical expression, derived from the torsional dynamics of DNA, to the extrapolated anisotropy decay. The second ethidium molecule binds to the same DNA segment which explains the decrease of A'0 by fast excitation energy transfer. At the same time theta 1 and theta 2 increase. On binding, a third ethidium molecule breaks the links between the DNA segment and the histone core. This entails the decrease of theta 1 and theta 2.
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14
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Genest D, Wahl P. An interpretation of the binding of ethidium bromide to the core nucleosome, based on Monte Carlo calculations. Biochimie 1981; 63:561-4. [PMID: 7260176 DOI: 10.1016/s0300-9084(81)80089-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We propose a model of ethidium binding to the nucleosome core particle. Ligand molecules are assumed to intercalate between the base pairs of the DNA core particle. The DNA is assumed to be divided into a finite number of segments. In the native core particle, one segment only is accessible to ethidium. The other DNA segments become progressively accessible when the binding ratio is increased. The binding isotherm resulting from such a model has been determined by a Monte Carlo method. The computed Scatchard plot exhibits the shape characteristic of a cooperative process. By fitting this curve with the experimental data of Erard et al. [1] one finds that 130 over the 140 DNA base pairs are accessible to the ethidium binding. The full accessibility of these sites is obtained when 8 or 9 ethidium at least are already bound to the core particle.
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15
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Mukhopadhyay R, Mookerjee A. Effect of gamma irradiation on dye-DNH binding. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1981; 39:143-55. [PMID: 6971826 DOI: 10.1080/09553008114550161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This paper attempts to analyse the effect of (a) gamma radiation and (b) the presence of histones in the form of nucleohistones (DNH) on the modes of ligand (Proflavine, Pf) binding to DNH. Effects were investigated by spectrophotometry. A certain dose of radiation which causes appreciable DNA denaturation has much less effect on DNH. There is a 'threshold' dose beyond which DNH denaturation is directly proportional to dose as in the case of DNA. The histones in DNH act as a shield and at higher doses get dissociated to expose the double helix to radiations. Ligand binding has a further stabilizing effect against radiation damage to DNH.
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Genest D, Sabeur G, Wahl P, Aubel-Sadron G. Location of the ethidium binding sites of high affinity in chromatin. Biophys Chem 1981; 13:89-96. [PMID: 7260330 DOI: 10.1016/0301-4622(81)80028-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The influence of H1 and H5 histones proteins upon the accessibility of ethidium bromide into chromatin is studied by steady-state fluorescence anisotropy in the range of r-values ([Dye]/[Phosphate]) smaller than 0.01. This corresponds to the very strong binding process. When H1 and H5 are present, the DNA segment which contains the binding sites is 25-30 base pairs long, even if H1 and H5 are digested by trypsin or by natural proteolysis, but presumably still interacting with the DNA chromatin. On the contrary, when H1 or H5 are separated from chromatin by an increase of the ionic strength, ethidium binds to a segment of DNA about 55-60 base pairs long. We may explain the results by assuming that the ethidium sites are located on a continuous segment constituting about one half of the linker, the other half interacting with H1 and H5. When chromatin is depleted from these proteins, the high affinity sites are distributed all along the linker.
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Abstract
The fluorescence anisotropy decays of the chromatin ethidium complexes have been measured in solutions in which the dye was bound to the high affinity sites of the nucleosome DNA. Energy transfers between chromatin-bound ethidium molecules cause an increase of naked DNA-ethidium complexes. This result implies that the high affinity sites are clustered on a short nucleosomal DNA segment. Quantitative analysis of the experimental data by computer simulations of the energy transfer process, shows that these sites are gathered on a single nucleosomal DNA segment, 28 base pairs long. Such a segment probably belongs to the nucleosomal "linker", contributing about half of it.
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Sorscher SM, Bartholomew JC, Klein MP. The use of fluorescence correlations spectroscopy to probe chromatin in the cell nucleus. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 610:28-46. [PMID: 6254568 DOI: 10.1016/0005-2787(80)90053-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
All systems in thermodynamic equilibrium are subject to spontaneous fluctuations from equilibrium. For very small system, the fluctuations can be made apparent, and can be used to study the behavior of the system without introducing any external perturbations. The mean squared amplitude of these fluctuations contains information about the absolute size of the system. The characteristic time of the fluctuation autocorrelation function contains kinetic information. In the experiments reported here, these concepts are applied to the binding equilibrium between ethidium bromide and DNA, a system where the fluorescence properties of the dye greatly enhance the effect of spontaneous fluctuations in the binding equilibrium. Preliminary experiments employ well-characterized DNA preparations, including calif thymus DNa, SV40 DNA, and calf thymus nucleohistone particles. Additional measurements are described which have been made in small regions of individual nuclei, isolated from green monkey kidney cells, observing as few as 5000 dye molecules. The data indicate that the strength of dye binding increases in nuclei isolated from cells which have been stimulated to enter the cell growth cycle. The viscosity of nuclear material is inferred to be between one and two orders of magnitude greater than that of water, and it decreases as the cells leave the resting state and enter the cell growth cycle. Washing the nuclei also lowers the viscosity. These experiments demonstrate that fluorescence correlation spectroscopy can provide information at the subnuclear level that is otherwise unavailable.
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Zunino F, Di Marco A, Zaccara A, Gambetta RA. The interaction of daunorubicin and doxorubicin with DNA and chromatin. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 607:206-14. [PMID: 7370266 DOI: 10.1016/0005-2787(80)90073-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Isotherms that describe the binding of anthracycline antibiotics (including daunorubicin and doxorubicin (adriamycin)) to calf thymus DNA and chromatin have been obtained by means of fluorescence measurements. As expected for charged ligands, the association constants for the interaction of all drugs examined with DNA were found to be dependent on the ionic strength. However, in the case of the daunorubicin-DNA interaction, a marked decrease in the number of binding sites was also observed when the ionic strength was increased. It is suggested that the effect of salt concentration on the number of potential binding sites of daunorubicin molecules to DNA may be the result of some salt-induced alterations in the DNA conformation. This interpretation is also supported by binding data obtained with calf thymus chromatin; Whereas at low salt concentration the binding parameters for the doxorubicin-chromatin interaction are similar to those expected by neutralization of the phosphate groups by histones, modifications of the DNA structure in chromatin are invoked to account for the reduction and heterogeneity of daunorubicin binding sites. The side chain at C-9 could play an important role in determining the strength and specificity of the anthracycline-DNA interaction.
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Paoletti J. Relaxation of chromatin structure induced by ethidium binding. Involvement of the intercalation process. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 100:531-9. [PMID: 510297 DOI: 10.1111/j.1432-1033.1979.tb04199.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this paper we study the effects of the binding of ethidium on the structure of chromatin, using micrococcal nuclease as a structural probe. This binding induces two structural changes of chromatin either isolated or in the nuclei. (a) An unfolding of the overall structure which results in an activation of the rate of degradation by the nuclease. (b) A disorganisation of the core particle structure which has the effect of unwrapping the DNA from the histone core, this disruption can go on so far as to leave only 90 base pairs. By comparing the bindings of ethidium and tetramethylethidium, we conclude that the first type of structural change is due to an electrostatic effect and does not depend upon intercalation. On the other hand, the second one is due to the intercalation process and to the change of topological constraints on the DNA that such a process involves.
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Flow microfluorometric analysis of nuclear DNA in cells from solid tumors and cell suspensions. ACTA ACUST UNITED AC 1977. [DOI: 10.1007/bf02889282] [Citation(s) in RCA: 129] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Graves DE, Yielding LW, Watkins CL, Yielding KL. Synthesis, separation and characterization of the mono- and diazide analogs of ethidium bromide. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 479:98-104. [PMID: 911852 DOI: 10.1016/0005-2787(77)90129-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ethidium bromide is used to characterize nucleic acid secondary and tertiary structural properties and the biological consequences of drug interactions. The mono- and diazido analogs of ethidium have proven valuable as photoaffinity probes in chemical and biological studies on nucleic acids, since they render the ethidium-nucleic acid interaction covalent. Although both of these compounds have been synthesized previously, the published synthesis procedure for the monoazide is inadeqlate since a major portion of the product has been identified as the diazide analog. This lack of purity severely limits the usefulness for nucleic acid research. The procedure presented here for the synthesis, separation, purification and crystallization of these analogs should provide the quantities and quality of these important reagents needed to perform a variety of chemical and biological experiments.
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25
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Doenecke D. Ethidium bromide (EB) binding to nucleosomal DNA. Effects on DNA cleavage patterns. Exp Cell Res 1977; 109:309-15. [PMID: 913495 DOI: 10.1016/0014-4827(77)90010-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
Addition of the intercalating dye quinacrine to a low ionic strength solution of DNA in quantities sufficient to saturate the high affinity sites in the DNA will result in the accumulation of the DNA at the solution interface. This entrapment of DNA at the air-water interface has been assayed by the adsorption of DNA to untreated carbon-coated electron microscope grids touched to the solution surface. Other intercalating dyes can also bring about this entrapment, if they possess a side arm large enough to occupy one of the DNA grooves when the dye is intercalated into the DNA. The extension and unwinding of the DNA helix brought about by the intercalating chromophore of the dye molecules are not requirements for the entrapment process. Spermidine, a simple polyamine that will bind to the DNA minor groove but that has no intercalating chromophore, was found to bring about this entrapment. Even simple mono- and divalent cations in the absence of the above ligands were found to promote a low level of surface entrapment. A model for the entrapment of DNA at the air-water interface is proposed in which one (or both) of the hydrophobic grooves of the DNA becomes a surface-active agent as a consequence of the association of various ligands and charge neutralization.
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LaRue H, Pallotta D. A study of the interaction between ethidium bromide and rye chromatin: comparison with calf thymus chromatin. Nucleic Acids Res 1976; 3:2193-206. [PMID: 987580 PMCID: PMC343076 DOI: 10.1093/nar/3.9.2193] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change in the binding of ethidium bromide. The subsequent extraction of H2A and H2B produces a 14% increase in the binding, and the removal of H3 and H4, another 54% increase. At this stage, the number of binding sites is still less than that of DNA. This is presumably due to the presence of some tightly bound non-histones. Thus, the arginine-rich histones and the tightly bound non-histones are most responsible for limiting the binding of ethidium bromide to rye chromatin.
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Huang CH, Baserga R. Circular dichroism studies of ethidium bromide binding to the isolated nucleolus. Nucleic Acids Res 1976; 3:1857-73. [PMID: 967680 PMCID: PMC343045 DOI: 10.1093/nar/3.8.1857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Circular dichroism in the 300-360 nm region and fluorescence induced by intercaltating binding of ethidum bromide to both DNA and RNA components were studied in isolated HeLa nucleoli. Both DNA and RNA compoents contribute to the induced dichroic elliticity. Digestion of nucleoli by RNase or DNase shows that most of the induced ellipticity comes from the DNA component. In nucleoli with an RNA/DNA = 0.8/1.0 the RNA component gives only 20% of the total ellipticity when measured at an ethidium bromide/DNA = 0.25. Spectro-fluorometric titration shows that ethidium bromide intercalates mostly into DNA in nucleoli. Both circular dichroism and fluorescence studies indicate that both DNA and RNA components in isolated nucleoli are less accessible to intercalating binding by ethidium bromide when compared to purified nucleolar DNA, DNA in chromatin or purified ribosomal RNA. Circular dichroic measurements of intercalating binding of ethidium bromide to to nucleoli may be used to study changes in nucleoli under different physiological or pathological conditions.
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Lawrence JJ, Daune M. Ethidium bromide as a probe of conformational heterogeneity of DNA in chromatin. The role of histone H1. Biochemistry 1976; 15:3301-7. [PMID: 952858 DOI: 10.1021/bi00660a021] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The accessibility and the tertiary structure of the DNA inside chromatin were studied by using ethidium bromide (EB) as a fluorescent probe. The exclusion model of binding was refined by introductina a parameter alpha (0less than alpha less than 1) which measures the accessibility of the DNA and by taking into account when necessary the existence of two sets of binding sites. We were thus able to fit predicted and experimental isotherms and then to describe completely EB binding to native or partially histone depleted chromatin under various conditions. Itn native chromatin 95% of the DNA (alpha = 0.95) appears to be accessible to EB but two sets of sites are present. The first one corresponds to alpha = 0.13 and is characterized by an affinity constant which is higher by two orders of magnitude than that relative to pure DNA. The second set corresponds to alpha = 0.82 and the corresponding binding constant is only three or four times lower than that of pure DNA. The sites with high affinity are still present after treatment with formaldehyde but disappear after removal of histon H1. By comparison with chromatin treated with deoxycholate of with artifical complexes between H1 and DNA, high affinity sites were found only when all of the histons are bound to DNA. An alpha value around 0.8 is still obtained in 1 M NaC1 treated chromatin, pointing to the fact that histones H3 and H4 are preventing 20% of the DNA to intercalate EB.
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Abstract
Actinomycin D (AMD) and ethidium bromide (EB) were found to bind to chromatin isolated from a variety of gander tissues according to a strong and weak process analogous to that found for deproteinized DNA. Distribution of the dye intercalation sites in chromatin and DNA were evaluated at low r-values (dye bound per nucleotide) by following the appearance of free dye released from chromatin and DNA during thermal denaturation. The AMD dissociation profiles closely resembled the DNA or chromatin-DNA denaturation profiles; whereas the EB derivative dissociation profiles, indicated 3 major transitions for transcriptionally active chromatin with the main component corresponding to the single component which characterizes DNA. The DNA-like component was greatly reduced for mature erythrocyte chromatin but could be generated by removal of histone I and V. Removal of residual non acid-soluble proteins from dehistonized chromatin, urea treatment or dissociation and reconstitution of chromatin favoured conversion to the DNA-like component with loss of the other two. This study indicates that more than one type of binding exists generally in chromatin.
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Nicolini C, Baserga R. Circular dichroism and ethidium bromide binding studies of chromatin from WI-38 fibroblasts stimulated to proliferate. Chem Biol Interact 1975; 11:101-16. [PMID: 1139738 DOI: 10.1016/0009-2797(75)90017-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Confluent monolayers of WI-38 diploid fibroblasts can be stimulated to proliferate by fresh serum. In the first 3 h after stimulation (that is, several hours before DNA replication) the chromatin of stimulated cells show structrual changes which include: (1) an increase in maximum positive ellipticity and a blue shift in the 250-300 nm region of circular dichroism spectra; and (2) an increase,in isolated chromatin, of the number of binding sites for the intercalating dye, ethidium bromide.The differences between chromtin of stimulated and chromatin of unstimulated cells are abolised when bother chromatins are treated with 0.25 M NaCL.
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Bontemps J, Houssier C, Fredericq E. Physico-chemical study of the complexes of "33258 Hoechst" with DNA and nucleohistone. Nucleic Acids Res 1975; 2:971-84. [PMID: 1144069 PMCID: PMC343483 DOI: 10.1093/nar/2.6.971] [Citation(s) in RCA: 94] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The degree of binding of "33258 Hoechst" to DNA and nucleohistone has been determined by equilibrium dialysis and the properties of the complexes have been followed by different optical and electro-optical methods, after determining the orientation of the main transition moments within the dye molecule. The binding isotherm was found composed of a Langmuir-type and of a strongly cooperative component. The existence of two bound species yielded a continuous variation of most of the properties of the complexes studied as the amount of binding increased, while the hydrodynamic properties of the macromolecules were not affected. At low binding, the strongly bound dye molecules appeared to bind to highly fluorescent sites with their long axis oriented at 45 degree to the helix axis. As the binding proceeds, less fluorescent sites are cooperatively occupied and the inclination of these ligand molecules becomes closer to that of the base planes. These results are compatible with the formation of two external complexes with the double helical structure.
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Brodie S, Giron J, Latt SA. Estimation of accessibility of DNA in chromatin from fluorescence measurements of electronic excitation energy transfer. Nature 1975; 253:470-1. [PMID: 1110800 DOI: 10.1038/253470a0] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Bontemps J, Houssier C, Fredericq E. Optical and electro-optical properties of the complexes of dibutylproflavine with DNA and nucleohistone. Biophys Chem 1974; 2:301-15. [PMID: 4474892 DOI: 10.1016/0301-4622(74)80057-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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