1
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Usta HM, Forough M, Persil Çetinkol Ö. Coumarin 6H-fused fluorescent probe for highly sensitive detection of coralyne using oligonucleotide-modified silver nanoparticles. Anal Bioanal Chem 2022; 414:7299-7313. [PMID: 35976422 DOI: 10.1007/s00216-022-04282-2] [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: 07/07/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022]
Abstract
In this study, a novel, rapid, and sensitive fluorescence sensing platform was developed for the detection of coralyne (COR) by the conjugation of coumarin 6H (C6H) fluorescent dye with oligonucleotide-modified silver nanoparticles [(dT)32-AgNPs]. In the presence of COR, a remarkable and rapid decrease in the fluorescence signal of the probe with a quenching efficiency of around 62% was observed. The quenching response of the system towards COR was possibly due to the displacement of thymidine-rich deoxyoligonucleotides by COR on the surface of AgNPs. The complementary experiments with an adenine-rich single strand as well as with two different secondary structures (i.e., duplex and triplex) revealed a favorable sequence specificity of the sensing platform. The influence of key parameters including the incubation time and temperature was evaluated and optimized to achieve the highest performance. The linear range of 10-183 nM with a correlation coefficient of R = 0.9982 and a limit of detection of 5.24 nM were obtained under the optimized conditions. The selectivity of the proposed probe towards COR was revealed by the evaluation of its response to other small molecules that have molecular structures similar to COR. Finally, the successful applicability of the system was shown with the obtained average recoveries in the range of 87.28-104.52% in human urine samples.
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Affiliation(s)
- Hatice Müge Usta
- Department of Chemistry, Middle East Technical University, 06800, Çankaya, Ankara, Turkey
| | - Mehrdad Forough
- Department of Chemistry, Middle East Technical University, 06800, Çankaya, Ankara, Turkey
| | - Özgül Persil Çetinkol
- Department of Chemistry, Middle East Technical University, 06800, Çankaya, Ankara, Turkey.
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2
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Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. ACS NANO 2022; 16:8954-8966. [PMID: 35640255 PMCID: PMC9649841 DOI: 10.1021/acsnano.1c11575] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyun Min Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Zhao P, Liu D, Hu H, Qiu Z, Liang Y, Chen Z. Anticancer activity of four trinuclear cobalt complexes bearing bis(salicylidene)-1,3-propanediamine derivatives. J Inorg Biochem 2022; 233:111860. [DOI: 10.1016/j.jinorgbio.2022.111860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/17/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
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4
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Lee C, Kim YJ, Kim KS, Lee JY, Kim DN. Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules. Nucleic Acids Res 2021; 49:12591-12599. [PMID: 34850119 PMCID: PMC8643692 DOI: 10.1093/nar/gkab1119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Kyung Soo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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5
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Rashid FZM, Mahlandt E, van der Vaart M, Boer DEC, Varela Alvarez M, Henneman B, Brocken DJW, Voskamp P, Blok A, Shimizu T, Meijer A, Luijsterburg M, Goedhart J, Crémazy FGE, Dame R. HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein. Nucleic Acids Res 2021; 50:e10. [PMID: 34734265 PMCID: PMC8789088 DOI: 10.1093/nar/gkab993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 02/02/2023] Open
Abstract
The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS — a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Eike Mahlandt
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Michiel van der Vaart
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Monica Varela Alvarez
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Bram Henneman
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Daan J W Brocken
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Patrick Voskamp
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Anneloes J Blok
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Thomas S Shimizu
- Systems Biology, AMOLF Institute, Amsterdam 1098XG, The Netherlands
| | - Annemarie H Meijer
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden 2333CC, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333ZC, The Netherlands
| | - Joachim Goedhart
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden 2333CC, The Netherlands
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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6
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Verma S, Ravichandiran V, Ranjan N, Flora SJS. Recent Advances in Therapeutic Applications of Bisbenzimidazoles. Med Chem 2021; 16:454-486. [PMID: 31038072 DOI: 10.2174/1573406415666190416120801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 12/16/2022]
Abstract
Nitrogen-containing heterocycles are one of the most common structural motifs in approximately 80% of the marketed drugs. Of these, benzimidazoles analogues are known to elicit a wide spectrum of pharmaceutical activities such as anticancer, antibacterial, antiparasitic, antiviral, antifungal as well as chemosensor effect. Based on the benzimidazole core fused heterocyclic compounds, crescent-shaped bisbenzimidazoles were developed which provided an early breakthrough in the sequence-specific DNA recognition. Over the years, a number of functional variations in the bisbenzimidazole core have led to the emergence of their unique properties and established them as versatile ligands against several classes of pathogens. The present review provides an overview of diverse pharmacological activities of the bisbenzimidazole analogues in the past decade with a brief account of its development through the years.
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Affiliation(s)
- Smita Verma
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli, 229010, India.,National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Vishnuvardh Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli, 229010, India
| | - Swaran J S Flora
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli, 229010, India
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7
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Zhang XX, Brantley SL, Corcelli SA, Tokmakoff A. DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site. Commun Biol 2020; 3:525. [PMID: 32963293 PMCID: PMC7508854 DOI: 10.1038/s42003-020-01241-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the dynamic interactions of ligands to DNA is important in DNA-based nanotechnologies. By structurally tracking the dissociation of Hoechst 33258-bound DNA (d(CGCAAATTTGCG)2) complex (H-DNA) with T-jump 2D-IR spectroscopy, the ligand is found to strongly disturb the stability of the three C:G base pairs adjacent to A:T the binding site, with the broken base pairs being more than triple at 100 ns. The strong stabilization effect of the ligand on DNA duplex makes this observation quite striking, which dramatically increases the melting temperature and dissociation time. MD simulations demonstrate an important role of hydration water and counter cations in maintaining the separation of terminal base pairs. The hydrogen bonds between the ligand and thymine carbonyls are crucial in stabilizing H-DNA, whose breaking signal appearing prior to the complete dissociation. Thermodynamic analysis informs us that H-DNA association is a concerted process, where H cooperates with DNA single strands in forming H-DNA.
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Affiliation(s)
- Xin-Xing Zhang
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA.
| | - Shelby L Brantley
- Department of Chemistry and Biochemistry, University of Norte Dame, Notre Dame, IN, 46556, USA
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Norte Dame, Notre Dame, IN, 46556, USA.
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL, 60637, USA
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8
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Fluorescent determination of micro-quantities of RNA using Hoechst 33258 and binase. Anal Biochem 2019; 576:5-8. [PMID: 30958999 DOI: 10.1016/j.ab.2019.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 11/20/2022]
Abstract
Detection of small amounts of RNA in various biological samples is an important applied task. Using fluorescence spectroscopy, the hydrolysis by binase of rRNA and tRNA, stained with Hoechst 33258, in aqueous solutions was investigated. The binding constant of Hoechst with rRNA is 106 M-1. Specific hydrolysis of rRNA and tRNA by binase during 1-2 min at room temperature leads to a multiple decrease in fluorescence of the dye. This rapid hydrolysis goes to large polynucleotide fragments, but not to short oligonucleotides. The binding constant of binase with rRNA is about of 2.5 × 106 M-1, which is several dozen times higher than with oligonucleotides. The susceptibility to binase attack depends on the secondary structure of RNA, determined by non-canonical ribonucleotides. The developed highly sensitive fluorescent method can be used for the rapid selective detection of trace amounts of rRNA or tRNA, as well as for studying the physicochemical properties of these RNAs. Using the proposed method, one can confidently detect RNA from 10-7 M.
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9
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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] [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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10
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Bucevičius J, Keller-Findeisen J, Gilat T, Hell SW, Lukinavičius G. Rhodamine-Hoechst positional isomers for highly efficient staining of heterochromatin. Chem Sci 2019; 10:1962-1970. [PMID: 30881625 PMCID: PMC6385482 DOI: 10.1039/c8sc05082a] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022] Open
Abstract
Hoechst conjugates to fluorescent dyes are popular DNA stains for live-cell imaging, but the relationship between their structure and performance remains elusive. This study of carboxyrhodamine-Hoechst 33258 conjugates reveals that a minimal change in the attachment point of the dye has dramatic effects on the properties of the final probe. All tested 6'-carboxyl dye-containing probes exhibited dual-mode binding to DNA and formed a dimmer complex at high DNA concentrations. The 5'-carboxyl dye-containing probes exhibited single-mode binding to DNA which translated into increased brightness and lower cytotoxicity. Up to 10-fold brighter nuclear staining by the newly developed probes allowed acquisition of stimulated emission depletion (STED) nanoscopy images of outstanding quality in living and fixed cells. Therefore we were able to estimate a diameter of ∼155 nm of the heterochromatin exclusion zones in the nuclear pore region in living cells and intact chicken erythrocytes and to localize telomeres relative to heterochromatin in living U-2 OS cells. Employing the highly efficient probes for two-color STED allowed visualization of DNA and tubulin structures in intact nucleated erythrocytes - a system where imaging is greatly hampered by high haemoglobin absorbance.
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Affiliation(s)
- Jonas Bucevičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Tanja Gilat
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Stefan W Hell
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Gražvydas Lukinavičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
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11
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Fritzsch R, Donaldson PM, Greetham GM, Towrie M, Parker AW, Baker MJ, Hunt NT. Rapid Screening of DNA–Ligand Complexes via 2D-IR Spectroscopy and ANOVA–PCA. Anal Chem 2018; 90:2732-2740. [DOI: 10.1021/acs.analchem.7b04727] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robby Fritzsch
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Paul M. Donaldson
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Michael Towrie
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Matthew J. Baker
- WestCHEM,
Department of Pure and Applied Chemistry, Technology and Innovation
Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, U.K
| | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
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12
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Wemyss AM, Chmel NP, Lobo DP, Sutherland JA, Dafforn TR, Rodger A. Fluorescence detected linear dichroism spectroscopy: A selective and sensitive probe for fluorophores in flow-oriented systems. Chirality 2018; 30:227-237. [PMID: 29314266 DOI: 10.1002/chir.22795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/22/2017] [Accepted: 10/27/2017] [Indexed: 11/06/2022]
Abstract
Fluorescence detection typically enhances sensitivity and selectivity for fluorescent analytes. The potential for combining fluorescence detection with flow orientation of the sample in the normal configuration of linear dichroism experiments is explored in this work by measuring the fluorescence emitted from flow-orientated DNA-bound ligands and M13 bacteriophage. Data for ethidium bromide, Hoechst 33258, and 4,6-diamidino-2-phenyindole are presented. The theoretical basis of the technique is also presented for instruments running in both the fixed direct-current mode, which is the normal operation mode of circular dichroism spectropolarimeters, and also in fixed high-tension voltage mode. The role of the stray light reaching the detector that results in a spectral shape in fixed direct current mode that resembles the shape of a linear dichroism spectrum, rather than the expected reduced linear dichroism, is also explored.
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Affiliation(s)
- Alan M Wemyss
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - Nikola P Chmel
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - Daniela P Lobo
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
| | - John A Sutherland
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia, USA
| | | | - Alison Rodger
- Department of Chemistry and MOAC Doctoral Training Centre, University of Warwick, Coventry, UK.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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13
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Ranjan N, Kellish P, King A, Arya DP. Impact of Linker Length and Composition on Fragment Binding and Cell Permeation: Story of a Bisbenzimidazole Dye Fragment. Biochemistry 2017; 56:6434-6447. [PMID: 29131946 DOI: 10.1021/acs.biochem.7b00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Small molecules that modulate biological functions are targets of modern day drug discovery efforts. In a common platform fragment-based drug discovery, two fragments that bind to adjacent sites on a target are identified and are then linked together using different linkers to identify the linkage for optimum activity. What are not known from these studies are the effects these linkers, which typically contain C, H, and O atoms, have on the properties of the individual fragment. Herein, we investigate such effects in a bisbenzimidazole fragment whose derivatives have a wide range of therapeutic applications in nucleic acid recognition, sensing, and photodynamic therapy and as cellular probes. We report a dramatic effect of linker length and composition of alkynyl (clickable) Hoechst 33258 derivatives in target binding and cell uptake. We show that the binding of Hoechst 33258-modeled bisbenzimidazoles (1-9) that contain linkers of varying lengths (3-21 atoms) display length- and composition-dependent variation in B-DNA stabilization using a variety of spectroscopic methods. For a dodecamer DNA duplex, the thermal stabilization varied from 0.3 to 9.0 °C as the linker length increased from 3 to 21 atoms, respectively. Compounds with linker lengths of ≤11 atoms (such as compounds 1 and 5) are localized in the nucleus, while compounds with long linkers (such as compounds 8 and 9) are distributed in the extranuclear space, as well, with possible interactions with extranuclear targets. These findings provide insights into future drug design by revealing how linkers can influence the biophysical and cellular properties of individual drug fragments.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Patrick Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Ada King
- NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States.,NUBAD LLC , 900 B West Faris Road, Greenville, South Carolina 29605, United States
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14
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Picconi P, Hind C, Jamshidi S, Nahar K, Clifford M, Wand ME, Sutton JM, Rahman KM. Triaryl Benzimidazoles as a New Class of Antibacterial Agents against Resistant Pathogenic Microorganisms. J Med Chem 2017. [PMID: 28650661 DOI: 10.1021/acs.jmedchem.7b00108] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A new class of nontoxic triaryl benzimidazole compounds, derived from existing classes of DNA minor groove binders, were designed, synthesized, and evaluated for their antibacterial activity against multidrug resistant (MDR) Gram-positive and Gram-negative species. Molecular modeling experiments suggest that the newly synthesized class cannot be accommodated within the minor groove of DNA due to a change in the shape of the molecules. Compounds 8, 13, and 14 were found to be the most active of the series, with MICs in the range of 0.5-4 μg/mL against the MDR Staphylococci and Enterococci species. Compound 13 showed moderate activity against the MDR Gram-negative strains, with MICs in the range of 16-32 μg/mL. Active compounds showed a bactericidal mode of action, and a mechanistic study suggested the inhibition of bacterial gyrase as the mechanism of action (MOA) of this chemical class. The MOA was further supported by the molecular modeling study.
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Affiliation(s)
- Pietro Picconi
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Charlotte Hind
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Kazi Nahar
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Melanie Clifford
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - Matthew E Wand
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - J Mark Sutton
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
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15
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Reis LA, Rocha MS. DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes. Biopolymers 2017; 107. [DOI: 10.1002/bip.23015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 01/10/2023]
Affiliation(s)
- L. A. Reis
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
| | - M. S. Rocha
- Laboratório de Física Biológica, Departamento de Física; Universidade Federal de Viçosa; Minas Gerais Brazil
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16
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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] [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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17
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Gomes A, Fernandes I, Teixeira C, Mateus N, Sottomayor MJ, Gomes P. A Quinacrine Analogue Selective Against Gastric Cancer Cells: Insight from Biochemical and Biophysical Studies. ChemMedChem 2016; 11:2703-2712. [PMID: 27863116 DOI: 10.1002/cmdc.201600477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/11/2016] [Indexed: 12/29/2022]
Abstract
One of the earliest synthetic antimalarial drugs, quinacrine, was recently reported as interesting for the treatment of acute myeloid leukemia. Inspired by this and similar findings, we evaluated a set of quinacrine analogues against gastric (MKN-28), colon (Caco-2), and breast (MFC-7) cancer cell lines and one normal human fibroblast cell line (HFF-1). All the compounds, previously developed by us as dual-stage antimalarial leads, displayed antiproliferative activity, and one of the set stood out as selective toward the gastric cancer cell line, MKN-28. Interestingly, this compound was transported across an in vitro MKN-28 model cell line in low amounts, and approximately 80 % was trapped inside those cells. Nuclear targeting of the same compound and its interactions with calf thymus DNA were assessed through combined fluorescence microscopy, spectroscopy, and calorimetry studies, which provided evidence for the compound's ability to reach the nucleus and to interact with DNA.
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Affiliation(s)
- Ana Gomes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Iva Fernandes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Cátia Teixeira
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Nuno Mateus
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - M J Sottomayor
- CIQ-UP, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Paula Gomes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
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18
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Amirbekyan K, Duchemin N, Benedetti E, Joseph R, Colon A, Markarian SA, Bethge L, Vonhoff S, Klussmann S, Cossy J, Vasseur JJ, Arseniyadis S, Smietana M. Design, Synthesis, and Binding Affinity Evaluation of Hoechst 33258 Derivatives for the Development of Sequence-Specific DNA-Based Asymmetric Catalysts. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00495] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karen Amirbekyan
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Nicolas Duchemin
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Erica Benedetti
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Rinah Joseph
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Aude Colon
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Shiraz A. Markarian
- Department
of Physical Chemistry, Yerevan State University, 1 Alex Manoogian, Yerevan 0025, Armenia
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Stephan Vonhoff
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Janine Cossy
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
| | - Jean-Jacques Vasseur
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
| | - Stellios Arseniyadis
- Laboratoire
de Chimie Organique, Institute of Chemistry, Biology and Innovation
(CBI) - ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University, 10 rue Vauquelin, 75231 CEDEX 05 Paris, France
- School
of Biological and Chemical Sciences, Queen Mary University of London, Joseph Priestley Building, Mile End Road, London E1 4NS, United Kingdom
| | - Michael Smietana
- Institut
des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM Place Eugène Bataillon, 34095 Montpellier, France
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19
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Xiong K, Blainey PC. Molecular sled sequences are common in mammalian proteins. Nucleic Acids Res 2016; 44:2266-73. [PMID: 26857546 PMCID: PMC4797294 DOI: 10.1093/nar/gkw035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/07/2016] [Indexed: 12/13/2022] Open
Abstract
Recent work revealed a new class of molecular machines called molecular sleds, which are small basic molecules that bind and slide along DNA with the ability to carry cargo along DNA. Here, we performed biochemical and single-molecule flow stretching assays to investigate the basis of sliding activity in molecular sleds. In particular, we identified the functional core of pVIc, the first molecular sled characterized; peptide functional groups that control sliding activity; and propose a model for the sliding activity of molecular sleds. We also observed widespread DNA binding and sliding activity among basic polypeptide sequences that implicate mammalian nuclear localization sequences and many cell penetrating peptides as molecular sleds. These basic protein motifs exhibit weak but physiologically relevant sequence-nonspecific DNA affinity. Our findings indicate that many mammalian proteins contain molecular sled sequences and suggest the possibility that substantial undiscovered sliding activity exists among nuclear mammalian proteins.
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Affiliation(s)
- Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
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20
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Busto N, Cano B, Tejido R, Biver T, Leal JM, Venturini M, Secco F, García B. Aggregation features and fluorescence of Hoechst 33258. J Phys Chem B 2015; 119:4575-81. [PMID: 25759973 DOI: 10.1021/jp512306c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functionality of the bisbenzimide Hoechst 33258 in solution has been largely exploited in the quantification of DNA. Understanding of its behavior is essential to promote its widespread application and learning of biological processes. A detailed study of the dimerization process of the fluorescent blue dye Hoechst 33258 is carried out by isothermal titration calorimetry, absorbance, fluorescence, differential scanning calorimetry and T-jump kinetic measurements. The dimer/monomer ratio depends on the dye concentration and the ionic strength. The dimerization constant determined under physiological conditions (pH = 7.0; I = 0.10 M), KD = 3 × 10(4) M(-1), conveys that only micromolar concentrations of the dye can ensure reasonably high amounts of the monomer species in solution. For instance, for 10 μM dye content, the dimer prevails for I > 0.08 M, whereas the monomer is observed at low ionic strength, a key issue to be elucidated as long as the dimer species is more fluorescent than the monomer and the fluorescence intensity strongly relies on the ionic strength and the dye concentration.
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Affiliation(s)
- Natalia Busto
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Beatriz Cano
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Rocío Tejido
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Tarita Biver
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - José M Leal
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
| | - Marcella Venturini
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Fernando Secco
- ‡Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56126 Pisa, Italy
| | - Begoña García
- †Departamento de Química, Universidad de Burgos, 09001 Burgos, Spain
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21
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Rocha MS. Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments. Integr Biol (Camb) 2015; 7:967-86. [DOI: 10.1039/c5ib00127g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review we focus on the idea of establishing connections between the mechanical properties of DNA–ligand complexes and the physical chemistry of DNA–ligand interactions.
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Affiliation(s)
- M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
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22
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Prisecaru A, Molphy Z, Kipping RG, Peterson EJ, Qu Y, Kellett A, Farrell NP. The phosphate clamp: sequence selective nucleic acid binding profiles and conformational induction of endonuclease inhibition by cationic Triplatin complexes. Nucleic Acids Res 2014; 42:13474-87. [PMID: 25414347 PMCID: PMC4267626 DOI: 10.1093/nar/gku1157] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 01/27/2023] Open
Abstract
The substitution-inert polynuclear platinum(II) complex (PPC) series, [{trans-Pt(NH3)2(NH2(CH2)nNH3)}2-μ-(trans-Pt(NH3)2(NH2(CH2)nNH2)2}](NO3)8, where n = 5 (AH78P), 6 (AH78 TriplatinNC) and 7 (AH78H), are potent non-covalent DNA binding agents where nucleic acid recognition is achieved through use of the 'phosphate clamp' where the square-planar tetra-am(m)ine Pt(II) coordination units all form bidentate N-O-N complexes through hydrogen bonding with phosphate oxygens. The modular nature of PPC-DNA interactions results in high affinity for calf thymus DNA (Kapp ∼5 × 10(7) M(-1)). The phosphate clamp-DNA interactions result in condensation of superhelical and B-DNA, displacement of intercalated ethidium bromide and facilitate cooperative binding of Hoechst 33258 at the minor groove. The effect of linker chain length on DNA conformational changes was examined and the pentane-bridged complex, AH78P, was optimal for condensing DNA with results in the nanomolar region. Analysis of binding affinity and conformational changes for sequence-specific oligonucleotides by ITC, dialysis, ICP-MS, CD and 2D-(1)H NMR experiments indicate that two limiting modes of phosphate clamp binding can be distinguished through their conformational changes and strongly suggest that DNA condensation is driven by minor-groove spanning. Triplatin-DNA binding prevents endonuclease activity by type II restriction enzymes BamHI, EcoRI and SalI, and inhibition was confirmed through the development of an on-chip microfluidic protocol.
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Affiliation(s)
- Andreea Prisecaru
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ralph G. Kipping
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
| | - Erica J. Peterson
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
| | - Yun Qu
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nicholas P. Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA
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23
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Kumari R, Bhowmick S, Das N, Das P. Binding and interaction of di- and tri-substituted organometallic triptycene palladium complexes with DNA. J Biol Inorg Chem 2014; 19:1221-32. [DOI: 10.1007/s00775-014-1180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/13/2014] [Indexed: 01/08/2023]
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24
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Ahmad H, Wragg A, Cullen W, Wombwell C, Meijer AJHM, Thomas JA. From Intercalation to Groove Binding: Switching the DNA-Binding Mode of Isostructural Transition-Metal Complexes. Chemistry 2014; 20:3089-96. [DOI: 10.1002/chem.201304053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 12/10/2013] [Indexed: 11/06/2022]
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25
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Silva EF, Ramos EB, Rocha MS. DNA Interaction with Hoechst 33258: Stretching Experiments Decouple the Different Binding Modes. J Phys Chem B 2013; 117:7292-6. [DOI: 10.1021/jp403945e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. F. Silva
- Laboratório de Física
Biológica,
Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E. B. Ramos
- Laboratório de Física
Biológica,
Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M. S. Rocha
- Laboratório de Física
Biológica,
Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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26
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Garg D, Beribisky AV, Ponterini G, Ligabue A, Marverti G, Martello A, Costi MP, Sattler M, Wade RC. Translational repression of thymidylate synthase by targeting its mRNA. Nucleic Acids Res 2013; 41:4159-70. [PMID: 23423353 PMCID: PMC3627590 DOI: 10.1093/nar/gkt098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Resistance to drugs targeting human thymidylate synthase (TS) poses a major challenge in the field of anti-cancer therapeutics. Overexpression of the TS protein has been implicated as one of the factors leading to the development of resistance. Therefore, repressing translation by targeting the TS mRNA could help to overcome this problem. In this study, we report that the compound Hoechst 33258 (HT) can reduce cellular TS protein levels without altering TS mRNA levels, suggesting that it modulates TS expression at the translation level. We have combined nuclear magnetic resonance, UV-visible and fluorescence spectroscopy methods with docking and molecular dynamics simulations to study the interaction of HT with a region in the TS mRNA. The interaction predominantly involves intercalation of HT at a CC mismatch in the region near the translational initiation site. Our results support the use of HT-like compounds to guide the design of therapeutic agents targeting TS mRNA.
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Affiliation(s)
- Divita Garg
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
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27
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McKnight RE, Reisenauer E, Pintado MV, Polasani SR, Dixon DW. Substituent effect on the preferred DNA binding mode and affinity of a homologous series of naphthalene diimides. Bioorg Med Chem Lett 2011; 21:4288-91. [DOI: 10.1016/j.bmcl.2011.05.069] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 05/16/2011] [Accepted: 05/18/2011] [Indexed: 11/15/2022]
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28
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Xu C, Zhao C, Ren J, Qu X. pH-controlled reversible drug binding and release using a cytosine-rich hairpin DNA. Chem Commun (Camb) 2011; 47:8043-5. [PMID: 21677978 DOI: 10.1039/c1cc12594j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we report that a cytosine-rich DNA carrier, that oscillates between a hairpin and an i-motif structure in its response to pH variation, can be used as a drug binding and release device.
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Affiliation(s)
- Can Xu
- Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun, Jilin 130022, China
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29
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Largy E, Hamon F, Teulade-Fichou MP. Development of a high-throughput G4-FID assay for screening and evaluation of small molecules binding quadruplex nucleic acid structures. Anal Bioanal Chem 2011; 400:3419-27. [PMID: 21528379 DOI: 10.1007/s00216-011-5018-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/08/2011] [Accepted: 04/12/2011] [Indexed: 11/25/2022]
Abstract
G4-FID (G-quadruplex fluorescent intercalator displacement) is a simple and fast method that allows to evaluate the affinity of a compound for G-quadruplex DNA and its selectivity towards duplex DNA. This assay is based on the loss of fluorescence of thiazole orange (TO) upon competitive displacement from DNA by a putative ligand. We describe here the development of a high-throughput version of this assay performed in 96-well microplates, and fully transposable to 384-well microplates. The test was calibrated with a set of G-quadruplex ligands characterized for their ability to bind quadruplex within a large range of affinity. The comparison of the results obtained in microplates and in cuvettes was conducted indicating a full agreement. Additionally, the spectral range of the test was enlarged using two other fluorescent on/off probes whose absorption are red-shifted (TO-PRO-3) and blue-shifted (Hoechst 33258) as compared to that of TO. These labels enable to screen a large diversity of compounds with various optical properties, which was exemplified by evaluation of affinity and selectivity of the porphyrin TMPyP4 that could not be evaluated previously. Altogether, our study demonstrates that the HT-G4-FID assay offers the possibility to label a large variety of G-quadruplexes of biological interest and should enable screening of collections of putative G4-ligands of high structural diversity. It thus represents a powerful tool to bring into light new ligands able to discriminate between quadruplexes of different structures.
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Affiliation(s)
- Eric Largy
- Institut Curie, CNRS UMR-176, Centre Universitaire, Orsay, France
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30
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Ramakrishnan S, Suresh E, Riyasdeen A, Akbarsha MA, Palaniandavar M. DNA binding, prominent DNA cleavage and efficient anticancer activities of tris(diimine)iron(II) complexes. Dalton Trans 2011; 40:3524-36. [PMID: 21369607 DOI: 10.1039/c0dt00466a] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The complexes rac-[Fe(diimine)(3)](ClO(4))(2)1-4, where diimine = 2,2'-bipyridine (bpy) 1, 1,10-phenanthroline (phen) 2, 5,6-dimethyl-1,10-phenanthroline (5,6-dmp) 3 and dipyrido[3,2-d:2',3'-f]quinoxaline (dpq) 4, have been isolated, characterized and their interaction with calf thymus DNA studied by using a host of physical methods. The X-ray crystal structure of rac-[Fe(5,6-dmp)(3)](ClO(4))(2)3 has been determined and the packing diagram shows the presence of two enantiomeric forms of the complex cations in the same unit cell. The structures of 1-4 in solution have also been studied using UV-Visible, Cyclic Voltammetry and ESI-MS data and all data available suggests that they retain their solid state structures even in solution. The absorption spectral titrations of the iron(ii) complexes with CT DNA reveal that the DNA binding affinities of the complexes vary in the order, 4 (K(b): 9.0 × 10(3)) > 2 (6.8 × 10(3)) > 3 (4. 8 × 10(3)) > 1 (2.9 × 10(3) M(-1)). The DNA interaction of dpq complex (4) involves partial insertion of the extended phen ring in between the DNA base pairs, which is deeper than that of phen (2). The 5,6-dmp (3) complex is involved in groove binding in the major groove of DNA. The lower DNA binding affinity of 1 is due to electrostatic interaction of the cationic complexes with exterior phosphates of DNA. The EthBr displacement assay and DNA viscosity study support these DNA binding modes and the above trend in DNA binding affinities. The complexes of 1 and 2 show induced CD (ICD) upon interaction with CT DNA while 3 and 4 bound to DNA exhibit inversion in the positive band with the helicity band showing very small changes, which implies that 3 and 4 bind enantiopreferentially to DNA. The DNA cleavage abilities of 1-4 have been observed at 10 μM concentration of complexes in the presence of 100 μM H(2)O(2) and the DNA cleavage efficiency (> 90%) follows the order 3 > 1 > 2 > 4. The anticancer activity of 1-4 against human breast cancer cell line (MCF-7) has also been studied. The IC(50) values of the complexes at different incubation time intervals of 24 and 48 h follow the order, 3 (0.8, 0.6) < 4 (20.0, 17.0) < 2 (28.0, 22.0) < 1 (32.0, 29.0 μM). Interestingly, 3 exhibits anticancer activity more potent than 1, 2 and 4 and cisplatin for both 24 and 48 h. It induces cell death both through apoptosis and necrosis mechanisms, as revealed by morphological assessment data obtained by using AO/EB and Hoechst 33258 fluorescence staining methods.
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Affiliation(s)
- Sethu Ramakrishnan
- Center for Bioinorganic Chemistry, School of Chemistry, Bharathidasan University, Tiruchirappalli, 620 024, Tamilnadu, India
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Sinha R, Hossain M, Kumar GS. Interaction of small molecules with double-stranded RNA: spectroscopic, viscometric, and calorimetric study of hoechst and proflavine binding to PolyCG structures. DNA Cell Biol 2009; 28:209-19. [PMID: 19364280 DOI: 10.1089/dna.2008.0838] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Design and synthesis of new small molecules binding to double-stranded RNA necessitate complete understanding of the molecular aspects of the binding of many existing molecules. Toward this goal, in this work we evaluated the biophysical aspects of the interaction of a DNA intercalator (proflavine) and a minor groove binder (hoechst 33258) with two polymorphic forms of polyCG, namely, the right-handed Watson-Crick base paired A-form and the left-handed Hoogsteen base paired H(L)-form, by absorption, fluorescence, and viscometry experiments. The energetics of the interaction of these molecules with the RNA structures has also been elucidated by isothermal titration calorimetry (ITC). Results suggest that proflavine strongly intercalates in both forms of polyCG, whereas hoechst shows mainly groove-binding modes. The binding of both drugs to both forms of RNA resulted in significant conformational change to the RNA structure with the bound molecules being placed in the chiral RNA helix. ITC profiles for both proflavine and hoechst show two binding sites. Binding of proflavine to both forms of RNA is endothermic and entropy driven in the first site and exothermic and enthalpy driven in the second site, whereas hoechst binding to both forms of RNA is exothermic and enthalpy driven in the first site and endothermic and entropy driven in the second site. This study suggests that the binding affinity characteristics and energetics of interaction of these DNA binding molecules with the RNA conformations are significantly different and may serve as data for future development of effective structure-selective RNA-based drugs.
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Affiliation(s)
- Rangana Sinha
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India.
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Ojha H, Murari BM, Anand S, Hassan MI, Ahmad F, Chaudhury NK. Interaction of DNA Minor Groove Binder Hoechst 33258 with Bovine Serum Albumin. Chem Pharm Bull (Tokyo) 2009; 57:481-6. [DOI: 10.1248/cpb.57.481] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Himanshu Ojha
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
| | | | - Sneh Anand
- Center for Biomedical Engineering, Indian Institute of Technology
| | | | - Faizan Ahmad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia
| | - Nabo Kumar Chaudhury
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences
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Xu Y, Afonso C, Wen R, Tabet JC. Investigation of double-stranded DNA/drug interaction by ESI/FT ICR: orientation of dissociations relates to stabilizing salt bridges. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1531-1544. [PMID: 18521852 DOI: 10.1002/jms.1430] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Noncovalent complexes of DNA and Hoechst 33258 were investigated by ESI-FT/ICR MS in various activation modes (collision-induced dissociation (CID), sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD) and electron detachment dissociation (EDD)). The binding selectivity of Hoechst 33258 was confirmed by the comparative study of its noncovalent association with different DNA sequences. The CID spectra of [ds + HO - 5H](5-) obtained with a linear hexapole ion trap resulted in unzipping of the strands. This outcome is a clue to the drug-binding mode, shading light on the localization of the binding sites of Hoechst 33258 to the DNA sequence. The IRMPD and SORI-CID experiments mainly gave DNA backbone cleavages and internal fragment ions. From this result, information on the localization of the binding sites of Hoechst 33258 in the DNA sequence was obtained. No sodium cationization was observed on the DNA sequence ions although they were present on fragmentation of the duplex, indicating that the backbone cleavages were generated from the single strand associated with the Hoechst 33258 where the number of alkali cation is restricted. Under electron detachment (ED) conditions, multiple EDs were achieved for the [ds + HO - 5H](5-) ion without any significant dissociation. The presence of drug appears to enhance the stability of the multiply charged system. It was proposed that the studied noncovalent complex involved the formation of zwitterions and consequently strong salt-bridge interactions between DNA and drug.
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Affiliation(s)
- Ying Xu
- Université Pierre et Marie Curie-Paris 6, UMR 7613 Synthèse, Structure et Fonction de Molécules Bioactives, Paris, F-75005, France
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Streltsov SA, Zhuze AL. Hoechst 33258--poly(dG-dC).poly(dG-dC) complexes of three types. J Biomol Struct Dyn 2008; 26:99-114. [PMID: 18533731 DOI: 10.1080/07391102.2008.10507228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
It was found recently that Hoechst 33258, a dsDNA fluorescent dye used in cytological studies, is an efficient inhibitor of the interaction of TATA-box-binding protein with DNA, DNA topoisomerase I, and DNA helicases. In addition it proved to be a radioprotector. Biological activity of Hoechst 33258 may be associated with dsDNA complexes of not only monomeric, but also dimeric type. In this work, the Hoechst 33258 interaction with poly(dG-dC).poly(dG-dC) was studied using UV-vis and fluorescent spectroscopy, circular and flow-type linear dichroism. It was found that Hoechst 33258 formed with poly(dG-dC).poly(dG-dC) complexes of three types, namely, monomeric, dimeric, and, apparently, tetrameric, and their spectral properties were studied. Complexes of monomeric and dimeric types competed with distamycin A, a minor groove ligand, for binding to poly(dG-dC).poly(dG-dC). We proposed that Hoechst 33258 both monomers and dimers form complexes of the external type with poly(dG-dC).poly(dG-dC) from the side of the minor groove.
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Affiliation(s)
- S A Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia.
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Buurma NJ, Haq I. Calorimetric and spectroscopic studies of Hoechst 33258: self-association and binding to non-cognate DNA. J Mol Biol 2008; 381:607-21. [PMID: 18617189 DOI: 10.1016/j.jmb.2008.05.073] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Revised: 05/04/2008] [Accepted: 05/30/2008] [Indexed: 10/22/2022]
Abstract
Sequence and structure-specific molecular recognition of DNA by small molecules is an important goal in biophysical chemistry and drug discovery. Many candidate ligands possess flat aromatic surfaces and other molecular features that allow them to self-associate. In addition, non-specific binding to the target is a complicating feature of these interactions. Therefore, multiple equilibria are present and need to be accounted for in data analysis in order to obtain meaningful thermodynamic parameters. In order to address these issues we have systematically examined the bis-benzimidazole dye Hoechst 33258 (H33258) in terms of self-aggregation and binding to DNA oligonucleotides lacking any cognate minor groove A.T sites. This model system has been interrogated using isothermal titration calorimetry (ITC), circular dichroism (CD), fluorescence spectroscopy and pulsed gradient spin echo NMR. Three distinct binding events and ligand self-aggregation have been identified and, where possible, quantified. H33258 self-aggregation involves a step-wise aggregation mechanism, driven by stacking interactions. The DNA binding process includes two specific binding modes and non-specific DNA-templated H33258 stacking. We have written novel ITC data-fitting software (IC-ITC; freely available to the biophysics community), which simultaneously fits ligand aggregation and ligand-DNA binding. Here, this numerical analysis, which uses simulated annealing of complex calorimetric data representing multiple coupled equilibria, is described.
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Affiliation(s)
- Niklaas J Buurma
- Centre for Chemical Biology, The Department of Chemistry, The University of Sheffield, Dainton Building, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
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36
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DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action. Curr Opin Biotechnol 2007; 18:497-503. [DOI: 10.1016/j.copbio.2007.09.006] [Citation(s) in RCA: 518] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 09/20/2007] [Accepted: 09/22/2007] [Indexed: 12/20/2022]
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37
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Guan Y, Shi R, Li X, Zhao M, Li Y. Multiple Binding Modes for Dicationic Hoechst 33258 to DNA. J Phys Chem B 2007; 111:7336-44. [PMID: 17530793 DOI: 10.1021/jp066344e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of dicationic Hoechst 33258 (ligand) to DNA was characterized by means of the fluorescence spectra, fluorescence intensity titration, time-resolved fluorescence decay, light scattering, circular dichroism, and fluorescence thermal denaturation measurements, and two binding modes were distinguished by the experimental results. Type 1 binding has the stoichiometry of one ligand to more than 12 base pairs, and it is defined as quasi-minor groove binding which has the typical prolonged fluorescence lifetime of about 4.4 ns. In type 1 binding, planar conformation of the ligand is favorable. Type 2 binding with phosphate to ligand ratio (P/L) < 2.5 has the stoichiometry of one ligand to two phosphates. It is defined as a highly dense and orderly stacked binding with DNA backbone as the template. Electrostatic interactions between doubly protonated ligands and negatively charged DNA backbone play a predominant role in the type 2 binding mode. The characteristics of this type of binding result in a twisted conformation of the ligand that has a fluorescence lifetime of less than 1 ns. The results also indicate that the binding is in a cooperative manner primarily by stacking of the aromatic rings of the neighboring ligands. Type 1 binding is only observed for double-stranded DNA (dsDNA) with affinity constant of 1.83 x 10(7) M-1. In the type 2 binding mode, the binding affinity constants are 4.9 x 10(6) and 4.3 x 10(6) M-1 for dsDNA and single-stranded DNA (ssDNA), respectively. The type 2 binding is base pair independent while the type 1 binding is base pair related. The experiments described in this paper revealed that the dication bindings are different from the monocation bindings reported by previous study. The dication binding leads to stronger aggregation at low ligand concentration and results in orderly arrangements of the ligands along DNA chains. Furthermore the dication binding is demonstrated to be beneficial for enhancing the DNA's stability.
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Affiliation(s)
- Yuan Guan
- The Key Laboratory of Bioorganic Chemistry & Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
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38
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Streltsov SA, Gromyko AV, Oleinikov VA, Zhuze AL. The Hoechst 33258 covalent dimer covers a total turn of the double-stranded DNA. J Biomol Struct Dyn 2007; 24:285-302. [PMID: 17054387 DOI: 10.1080/07391102.2006.10507121] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
With the goal to design ligands recognizing extended regions on dsDNA, a covalent dimer of the fluorescent dye Hoechst 33258 [bis-HT(NMe)] composed of two dye molecules linked via the phenol oxygen atoms with a (CH2)3-N+ H(CH3)-(CH2)3 fragment was constructed using computer modeling and then synthesized. Its interactions with the double-stranded DNA (dsDNA) were studied by fluorescent and UV-Vis spectroscopy and circular (CD) and linear dichroism (LD). Based on variations in the affinity to the dsDNA, it was shown that complexes of three types are formed. The first type complexes result from binding of a bis-HT(NMe) monomer in the open conformation; in this case the ligand covers the total dsDNA turn and is located in the minor groove according to the positive value of CD at 370 nm. In addition, the ability to form bis-HT(NMe)-bridges between two dsDNA molecules, i.e., each of the two bis-HT(NMe) ends binds to two different dsDNA molecules, was demonstrated for the first type complexes. Spectral characteristics (maximal absorption at 362 nm, positive sign, and maximal value of CD at 370 nm) of the first type complexes conform to those of the specific Hoechst 33258 complex with poly[d(A-T)] x poly[d(A-T]. The second type complexes correspond to the bis-HT(NMe) sandwich (as an inter- or intramolecular) binding to dsDNA with stoichiometry > or = 5 bp. Thereby, a negative LD at 360 nm and the location of bis-HT(NMe) sandwiches in the minor groove of B form dsDNA seems contradictory. Spectral characteristics (maximal positive CD at 345 nm, a dramatic decrease in fluorescence intensity and the shift of its maximum to 490 nm) of these complexes favor a suggestion that this binding correlates to the formation of nonspecific dimeric Hoechst 33258 complex with dsDNA. The third type complexes are characterized by stoichiometry of one bis-HT(NMe) molecule per approximately 2 bp and the tendency to zero of LD values at 270 and 360 nm. We assume that in these complexes bis-HT(NMe) sandwich dimers are formed on dsDNA. The complexes of this type conform to the aggregation type complex of Hoechst 33258 with dsDNA. The ability of bis-HT(NMe) to cover the whole dsDNA turn or form bridges with two dsDNA upon the formation of the first type complexes essentially distinguishes it from Hoechst 33258, which can only occupy 5 bp and does not form such bridges. This specific property of bis-HT(NMe) may support new biological activities.
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Affiliation(s)
- S A Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia.
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39
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McKnight RE, Gleason AB, Keyes JA, Sahabi S. Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay. Bioorg Med Chem Lett 2007; 17:1013-7. [PMID: 17157016 DOI: 10.1016/j.bmcl.2006.11.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 11/08/2006] [Accepted: 11/13/2006] [Indexed: 11/26/2022]
Abstract
A topoisomerase I DNA unwinding assay has been used to determine the relative DNA-binding affinities of a model pair of homologous naphthalene diimides. Binding affinity data were corroborated using calorimetric (ITC) and spectrophotometric (titration and T(m)) studies, with substituent size playing a significant role in binding. The assay was also used to investigate the mode of binding adopted by several known DNA-binding agents, including SYBR Green and PicoGreen. Some of the compounds exhibited unexpected binding modes.
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Affiliation(s)
- Ruel E McKnight
- Department of Chemistry, State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA.
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40
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Tonary AM, Pezacki JP. Simultaneous quantitative measurement of luciferase reporter activity and cell number in two- and three-dimensional cultures of hepatitis C virus replicons. Anal Biochem 2006; 350:239-48. [PMID: 16480942 DOI: 10.1016/j.ab.2006.01.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 12/20/2005] [Accepted: 01/09/2006] [Indexed: 11/25/2022]
Abstract
Hepatitis C virus (HCV) is a global health problem and an important human pathogen. The development of cell culture models for HCV infection has been difficult to accomplish, primarily because HCV is very sensitive to the host cell state. Future models will require the use of three-dimensional (3D) cultures that model the host cell state and environment more accurately. Higher information content screens for anti-HCV therapeutics will also involve 3D cell cultures. Here we report a method for screening cell models for HCV replication that involves normalizing luciferase reporter activity based on cell number in two-dimensional (2D) and 3D HCV replicon cultures. Human hepatoma cells stably replicating luciferase-containing HCV replicons were cultured in 2D monolayer culture and 3D spheroid culture. Optimization of cell lysis was performed so that cell lysates could be used to quantify both luciferase activity and cellular DNA content. Cellular DNA content was quantified using Hoechst 33258 dye and was converted to cell number. The method is straightforward, reproducible, and sensitive down to 5000 cells. This method enables low-throughput but high-information content screening of HCV replicons, with the potential for high-throughput screening in a variety of 3D cultures and cocultures.
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Affiliation(s)
- Angela M Tonary
- Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ont., Canada K1A 0R6
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41
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Kiser JR, Monk RW, Smalls RL, Petty JT. Hydration changes in the association of Hoechst 33258 with DNA. Biochemistry 2005; 44:16988-97. [PMID: 16363812 PMCID: PMC6158785 DOI: 10.1021/bi051769x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of water in the interaction of Hoechst 33258 with the minor groove binding site of the (AATT)2 sequence was investigated using calorimetric and equilibrium constant measurements. Using isothermal titration calorimetry measurements, the heat capacity change for the reaction is -256 +/- 10 cal/(K mol of Hoechst). Comparison with the heat capacity changes based on area models supports the expulsion of water from the interface of the Hoechst-DNA complex. To further consider the role of water, the osmotic stress method was used to determine if the Hoechst association with DNA was coupled with hydration changes. Using four osmolytes with varying molecular weights and chemical properties, the Hoechst affinity for DNA decreases with increasing osmolyte concentration. From the dependence of the equilibrium constant on the solution osmolality, 60 +/- 13 waters are acquired in the complex relative to the reactants. It is proposed that the osmotic stress technique is measuring weakly bound waters that are not measured via the heat capacity changes.
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Affiliation(s)
- John R Kiser
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
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42
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Keller KM, Zhang J, Oehlers L, Brodbelt JS. Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1362-71. [PMID: 16220501 DOI: 10.1002/jms.927] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The charge state-dependent dissociation of various DNA duplexes and drug/duplex complexes has been investigated using collisionally activated dissociation (CAD) in a quadrupole ion trap mass spectrometer (QIT-MS). Several non-self-complementary 14-residue oligonucleotides were employed, in addition to an array of known DNA-interactive ligands, including the intercalators daunomycin and nogalamycin, as well as the minor groove binding agents distamycin, netropsin, 4',6-diamidino-2-phenylindole, and Hoechst 33342. In general, the dissociation pathways exhibited by both the duplexes and the drug/duplex complexes were found to be markedly sensitive to initial charge state. Time- and activation voltage-independent duplex strand separation predominated for higher charge states, which was interpreted to be a result of internal Coulombic repulsion or partial unzipping in the interface, while time- and activation voltage-dependent covalent cleavage predominated for lower charge states. The identity of the drug and the sequence of the duplex were both found to affect the competition between different dissociation processes. The dissociation pathways for the lower charge state complexes are probably more reflective of specific drug-DNA interactions because Coulombic and/or conformational effects are less marked for these precursors.
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Affiliation(s)
- Karin M Keller
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin TX 78712, USA
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43
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Alemán C, Namba AM, Casanovas J. Acid-Base and Electronic Structure-Dependent Properties of Hoechst 33342. J Biomol Struct Dyn 2005; 23:29-36. [PMID: 15918674 DOI: 10.1080/07391102.2005.10507044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
An ab initio quantum mechanical study of the bis-benzimidazole derivative Hoechst 33342 is presented. Specifically, we report on the molecular geometry, proton affinity, gas-phase basicity, hydration, pKa, and molecular interaction potential map of Hoechst 33342 and the forms obtained by its protonation and deprotonation. Results have been compared with those obtained for Hoechst 33258 to analyze the influence of the chemical structure on the properties of this bis-benzimidazole derivative. Finally, the connection of some theoretical predictions with experimental evidences has been examined.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Quimica, E.T.S. d'Enginyeria Industrial de Barcelona, Universitat Politecnica de Catalunya, Barcelona E-08028, Spain.
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44
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Ladinig M, Leupin W, Meuwly M, Respondek M, Wirz J, Zoete V. Protonation Equilibria ofHoechst 33258 in Aqueous Solution. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200490296] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Karlsson HJ, Bergqvist MH, Lincoln P, Westman G. Syntheses and DNA-binding studies of a series of unsymmetrical cyanine dyes: structural influence on the degree of minor groove binding to natural DNA. Bioorg Med Chem 2004; 12:2369-84. [PMID: 15080934 DOI: 10.1016/j.bmc.2004.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Accepted: 02/03/2004] [Indexed: 11/28/2022]
Abstract
Twelve crescent-shaped unsymmetrical dyes have been synthesized and their interactions with DNA have been investigated by spectroscopic methods. A new facile synthetic route to this type of cyanine dyes has been developed, involving the preparation of 6-substituted 2-thiomethyl-benzothiazoles in good yields. The new dyes are analogues to the minor groove binding unsymmetrical cyanine dye, BEBO, recently reported by us. In this dye, the structure of the known intercalating cyanine dye BO was extended with a 6-methylbenzothiazole substituent. Herein we further investigate the role of the extending benzazole heterocycle, as well as of the pyridine or quinoline moiety of the cyanine chromophore, for the binding mode of these crescent-shaped dyes to calf thymus DNA. Flow LD and CD studies of the 12 dyes show that the extent of minor groove binding to mixed sequence DNA varies significantly between the dyes. We find that hydrophobicity and size are the crucial parameters for recognition of the minor groove. The relatively high fluorescence quantum yield of many of these cyanines bound to DNA, combined with their absorption at long wavelengths, may render them useful in biological applications. In particular, two of the benzoxazole containing dyes BOXTO and 2-BOXTO show a high degree of minor groove binding and quantum yields of 0.52 and 0.32, respectively, when bound to DNA.
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Affiliation(s)
- H Jonas Karlsson
- Department of Chemistry and Bioscience, Chalmers University of Technology, S-412 96 Gothenburg, Sweden.
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46
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Adhikary A, Buschmann V, Müller C, Sauer M. Ensemble and single-molecule fluorescence spectroscopic study of the binding modes of the bis-benzimidazole derivative Hoechst 33258 with DNA. Nucleic Acids Res 2003; 31:2178-86. [PMID: 12682368 PMCID: PMC153736 DOI: 10.1093/nar/gkg308] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ensemble and single-molecule fluorescence measurements of 2'-(4-hydroxyphenyl)-5-[5-(4-methylpiperazine-1-yl) benzimidazo-2-yl]-benzimidazole (H-258)- calf thymus (CT) DNA complexes at various [H-258]/[DNA bp] ratios were performed to elucidate the binding of H-258 with DNA. Upon binding to double-stranded CT DNA (CT ds DNA) at a [H-258]/[DNA bp] ratio of 0.05 the relative fluorescence quantum yield, Phi(f), of H-258 increases from 0.02 to 0.58. The fluorescence decay can be fitted almost by a mono-exponential model with a lifetime of approximately 3.6 ns. This indicates that H-258 binds almost quantitatively in the minor groove of DNA at low [H-258]/[DNA bp] ratios. With increasing [H-258]/[DNA bp] ratios, e.g. 0.15 and 0.20, the fluorescence quantum yield of H-258 decreases to 0.28 and 0.19, respectively. Fitting of the fluorescence decays measured for higher [H-258]/[DNA bp] ratios reveals the presence of additional shorter fluorescence lifetime components in the range of 0.5-2.0 ns. Our results suggest that H-258 partially intercalates in G:C sequences at higher [H-258]/[DNA bp] ratios reflected by a lifetime component of 1.5-2 ns. In addition, stacking or adsorption of H-258 molecules on DNA occurs at higher [H-258]/[DNA bp] ratios. These molecules exhibit a short fluorescence lifetime of approximately 500 ps and are more exposed to the aqueous environment. Fluorescence transients of the intensity and lifetime of single H-258 CT ds DNA demonstrate that weakly (unspecific) bound H-258 molecules exhibit a shorter fluorescence lifetime and a strongly reduced photostability.
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Affiliation(s)
- Amitava Adhikary
- Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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47
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Alemán C, Adhikary A, Zanuy D, Casanovas J. On the protonation equilibrium for the benzimidazole derivative Hoechst 33258: an electronic molecular orbital study. J Biomol Struct Dyn 2002; 20:301-10. [PMID: 12354081 DOI: 10.1080/07391102.2002.10506845] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Hoechst 33258 and its deprotonated forms have been examined in the gas-phase and in solution using quantum mechanical methods. Ab initio calculations at the HF level have been used to investigate the more relevant geometrical trends of such species, while proton affinities and gas-phase basicities were derived from B3LYP and MP2 electronic energies. Solvation energies were calculated using a dielectric continuum model: MST. The Delta(p)K(a) values were estimated by combining the gas-phase basicities and the free energies of solvation. Comparison of these Delta(p)K(a) values with experimentally reported data have been used to highlight the advantages and limitations of this strategy.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E.T.S. d'Enginyers Industrials de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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48
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Rosu F, Gabelica V, Houssier C, De Pauw E. Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry. Nucleic Acids Res 2002; 30:e82. [PMID: 12177310 PMCID: PMC134255 DOI: 10.1093/nar/gnf081] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Electrospray mass spectrometry was evaluated regarding the reliability of the determination of the stoichiometries and equilibrium association constants from single spectra. Complexes between minor groove binders (Hoechst 33258, Hoechst 33342, DAPI, netropsin and berenil) and 12mer oligonucleotide duplexes with a central sequence (A/T)4 flanked by G/C base pairs were chosen as model systems. To validate the electrospray ionization mass spectrometry (ESI-MS) method, comparisons were made with circular dichroism and fluorescence spectroscopy measurements. ESI-MS allowed the detection of minor (2 drug + DNA) species for Hoechst 33258, Hoechst 33342, DAPI and berenil with duplex d(GGGG(A/T)4GGGG). d(CCCC(A/T)4CCCC), which were undetectable with the other techniques. Assuming that the duplexes and the complexes have the same electrospray response factors, the equilbrium association constants of the 1:1 and 2:1 complexes were determined by ESI-MS, and the values show a good quantitative agreement with fluorescence determined constants for Hoechst 33258 and Hoechst 33342. It is also shown that ESI-MS can quickly give reliable information on the A/T sequence selectivity of a drug: the signal of a complex is directly related to the affinity of the drug for that particular duplex. The potential of ESI-MS as a qualitative and quantitative affinity screening method is emphasized.
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Affiliation(s)
- Frederic Rosu
- Biospectroscopy Laboratory, University of Liège, Chemistry Institute, Bâtiment B6c, B-4000 Liège, Belgium
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49
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Bielawski K, Bielawska A, Wołczyński S. Synthesis, DNA-binding activity and cytotoxicity of carbamate derivatives of Hoechst 33258 in breast cancer MCF-7 cells. Biol Pharm Bull 2002; 25:916-9. [PMID: 12132669 DOI: 10.1248/bpb.25.916] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of carbamate derivatives of Hoechst 33258 was prepared as potential anticancer agents. These new compounds (1-4) were readily prepared in good yields by addition of chloroethyl, bromoethyl, chloropropyl or 4-(chloromethyl)phenyl isocyanates to Hoechst 33258. Their cytotoxic activity was evaluated on human breast cancer MCF-7. Compounds 1-4 were more cytotoxic than Hoechst 33258. In particular derivative 4, the most active of the series, is up to 3 times more potent than Hoechst 33258. The DNA-binding ability of these compounds was evaluated by an ultrafiltration method using calf thymus DNA. These data show that in broad terms the cytotoxic potency of 1-4 in cultured breast cancer MCF-7 cells increases, in accord with their increases in DNA affinity, as shown by the binding constant values.
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Affiliation(s)
- Krzysztof Bielawski
- Department of Medicinal Chemistry and Drug Technology, Medical Academy of Białystok, Poland.
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50
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Utsuno K, Tsuboi M, Katsumata S, Iwamoto T. Visualization of complexes of Hoechst 33258 and DNA duplexes in solution by atomic force microscopy. Chem Pharm Bull (Tokyo) 2002; 50:216-9. [PMID: 11848212 DOI: 10.1248/cpb.50.216] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tertiary structure changes in DNA duplexes, induced by Hoechst 33258 binding, have been examined by the use of atomic force microscopy. Besides minor groove binding, which is an established mode of binding for this drug, Hoechst 33258 has now been found to show another binding mode, which causes an unwinding of the duplex. When the drug concentration is as high as 0.5 microg/ml, the Hoechst 33258 molecule seems to function as a clamp for two DNA chains and forms a condensate. The condensate was found to have a toroidal shape. By surveying more than 100 microscopic images of such condensates formed in I microg/ml drug solution, a mechanism of toroidal condensate formation has been proposed.
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Affiliation(s)
- Kuniharu Utsuno
- High-Tech Research Center, College of Science and Engineering, Iwaki Meisei University, Fukushima, Japan
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