1
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Nicholson DA, Nesbitt DJ. Kinetic and Thermodynamic Control of G-Quadruplex Polymorphism by Na + and K + Cations. J Phys Chem B 2023; 127:6842-6855. [PMID: 37504511 DOI: 10.1021/acs.jpcb.3c01001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
G-Quadruplexes (G4s) are ubiquitous nucleic acid folding motifs that exhibit structural diversity that is dependent on cationic conditions. In this work, we exploit temperature-controlled single-molecule fluorescence resonance energy transfer (smFRET) to elucidate the kinetic and thermodynamic mechanisms by which monovalent cations (K+ and Na+) impact folding topologies for a simple G-quadruplex sequence (5'-GGG-(TAAGGG)3-3') with a three-state folding equilibrium. Kinetic measurements indicate that Na+ and K+ influence G4 formation in two distinctly different ways: the presence of Na+ modestly enhances an antiparallel G4 topology through an induced fit (IF) mechanism with a low affinity (Kd = 228 ± 26 mM), while K+ drives G4 into a parallel/hybrid topology via a conformational selection (CS) mechanism with much higher affinity (Kd = 1.9 ± 0.2 mM). Additionally, temperature-dependent studies of folding rate constants and equilibrium ratios reveal distinctly different thermodynamic driving forces behind G4 binding to K+ (ΔH°bind > 0, ΔS°bind > 0) versus Na+ (ΔH°bind < 0, ΔS°bind < 0), which further illuminates the diversity of the possible pathways for monovalent facilitation of G-quadruplex folding.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
- Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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2
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Guan L, Mao Y, Zhou Y, Feng X, Fu, Yile. Research Progress in Cyanine-Based Recognition Probes for G-Quadruplex DNA. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202203025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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3
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Banerjee N, Panda S, Chatterjee S. Frontiers in G-Quadruplex Therapeutics in Cancer: Selection of Small Molecules, Peptides and Aptamers. Chem Biol Drug Des 2021; 99:1-31. [PMID: 34148284 DOI: 10.1111/cbdd.13910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022]
Abstract
G-quadruplex, a unique secondary structure in nucleic acids found throughout human genome, elicited widespread interest in the field of therapeutic research. Being present in key regulatory regions of oncogenes, RNAs and telomere, G-quadruplex structure regulates transcription, translation, splicing etc. Changes in its structure and stability leads to differential expression of oncogenes causing cancer. Thus, targeting G-Quadruplex structures with small molecules/other biologics has shown elevated research interest. Covering previous reports, in this review we try to enlighten the facts on the structural diversity in G-quadruplex ligands aiming to provide newer insights to design first-in-class drugs for the next generation cancer treatment.
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Affiliation(s)
- Nilanjan Banerjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Suman Panda
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
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4
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Laramie MD, Fouts BL, MacCuaig WM, Buabeng E, Jones MA, Mukherjee P, Behkam B, McNally LR, Henary M. Improved pentamethine cyanine nanosensors for optoacoustic imaging of pancreatic cancer. Sci Rep 2021; 11:4366. [PMID: 33623069 PMCID: PMC7902650 DOI: 10.1038/s41598-021-83658-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Optoacoustic imaging is a new biomedical imaging technology with clear benefits over traditional optical imaging and ultrasound. While the imaging technology has improved since its initial development, the creation of dedicated contrast agents for optoacoustic imaging has been stagnant. Current exploration of contrast agents has been limited to standard commercial dyes that have already been established in optical imaging applications. While some of these compounds have demonstrated utility in optoacoustic imaging, they are far from optimal and there is a need for contrast agents with tailored optoacoustic properties. The synthesis, encapsulation within tumor targeting silica nanoparticles and applications in in vivo tumor imaging of optoacoustic contrast agents are reported.
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Affiliation(s)
- Matthew D Laramie
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Benjamin L Fouts
- Department of Surgery, Oklahoma Health Science Center, Oklahoma City, 73104, USA
- Stephenson Cancer Center, Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
| | - William M MacCuaig
- Stephenson Cancer Center, Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
- Department of Biomedical Engineering, University of Oklahoma, Norman, OK, 72073, USA
| | - Emmanuel Buabeng
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Meredith A Jones
- Department of Biomedical Engineering, University of Oklahoma, Norman, OK, 72073, USA
| | - Priyabrata Mukherjee
- Department of Pathology, Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech University, Blacksburg, VA, 24061, USA
| | - Lacey R McNally
- Department of Surgery, Oklahoma Health Science Center, Oklahoma City, 73104, USA.
- Stephenson Cancer Center, Oklahoma Health Science Center, Oklahoma City, OK, 73104, USA.
- Department of Biomedical Engineering, University of Oklahoma, Norman, OK, 72073, USA.
- Department of Cancer Biology, Wake Forest University, Winston-Salem, NC, 27157, USA.
| | - Maged Henary
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA.
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5
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Chaudhuri R, Bhattacharya S, Dash J, Bhattacharya S. Recent Update on Targeting c-MYC G-Quadruplexes by Small Molecules for Anticancer Therapeutics. J Med Chem 2020; 64:42-70. [PMID: 33355454 DOI: 10.1021/acs.jmedchem.0c01145] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Guanine-rich DNA sequences have the propensity to adopt four-stranded tetrahelical G-quadruplex (G4) structures that are overrepresented in gene promoters. The structural polymorphism and physicochemical properties of these non-Watson-Crick G4 structures make them important targets for drug development. The guanine-rich nuclease hypersensitivity element III1 present in the upstream of P1 promoter of c-MYC oncogene has the ability to form an intramolecular parallel G4 structure. The G4 structure that forms transiently in the c-MYC promoter functions as a transcriptional repressor element. The c-MYC oncogene is overexpressed in a wide variety of cancers and plays a key role in cancer progression. Till now, a large number of compounds that are capable of interacting and stabilizing thec-MYC G4 have been reported. In this review, we summarize various c-MYC G4 specific molecules and discuss their effects on c-MYC gene expression in vitro and in vivo.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Semantee Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.,Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
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6
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Ahoulou EO, Drinkard KK, Basnet K, St. Lorenz A, Taratula O, Henary M, Grant KB. DNA Photocleavage in the Near-Infrared Wavelength Range by 2-Quinolinium Dicarbocyanine Dyes. Molecules 2020; 25:molecules25122926. [PMID: 32630496 PMCID: PMC7355653 DOI: 10.3390/molecules25122926] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
Here, we report the syntheses of two pentamethine cyanine dyes containing quinolinium rings and substituted with either hydrogen (3) or bromine (4) at the meso carbon. The electron withdrawing bromine atom stabilizes dye 4 in aqueous buffer, allowing complex formation to occur between the dye and double-helical DNA. UV–visible, CD, and fluorescence spectra recorded at low DNA concentrations suggest that dye 4 initially binds to the DNA as a high-order aggregate. As the ratio of DNA to dye is increased, the aggregate is converted to monomeric and other low-order dye forms that interact with DNA in a non-intercalative fashion. The brominated dye 4 is relatively unreactive in the dark, but, under 707–759 nm illumination, generates hydroxyl radicals that cleave DNA in high yield (pH 7.0, 22 °C). Dye 4 is also taken up by ES2 ovarian carcinoma cells, where it is non-toxic under dark conditions. Upon irradiation of the ES2 cells at 694 nm, the brominated cyanine reduces cell viability from 100 ± 10% to 14 ± 1%. Our results suggest that 2-quinolinium-based carbocyanine dyes equipped with stabilizing electron withdrawing groups may have the potential to serve as sensitizing agents in long-wavelength phototherapeutic applications.
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Affiliation(s)
- Effibe O. Ahoulou
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kaitlyn K. Drinkard
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kanchan Basnet
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Anna St. Lorenz
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Oleh Taratula
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Maged Henary
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
| | - Kathryn B. Grant
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
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7
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Pitigala PKDDP, Henary MM, Perera AGU. Effects of physical orientation of dye molecules and molecular orbitals on performance of solid-state dye sensitized solar cells. ACTA ACUST UNITED AC 2020; 23:43-48. [PMID: 33718004 DOI: 10.1016/j.matpr.2019.06.189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Performance of Dye-sensitized devices depends on the photon absorption and carrier injection properties of the sensitizer (dye). The orientation of the dye molecule affects the photon absorption cross-section, injection efficiency and carrier transport. These effects are studied, using three variants of cyanine dyes in n-TiO2/Dye/p-CuSCN heterojunction. The results show correlation of dye-molecule's orientation on the short-circuit-photocurrent (Isc). The open-circuit-voltage (Voc) is also subjective. The orientation of the dye molecule influence the photon-harvesting efficiency and obstruct the hole-conductor penetrating onto the working-electrode. Additionally, Cumulative effects of e-e, e-h, spin-coupling and HOMO/LUMO distribution are identified.
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Affiliation(s)
- P K D D P Pitigala
- Department of Physics, University of Sri Jayewardenepura, Gangodavila, Sri Lanka.,Center for Advance Material Research,, University of Sri Jayewardenepura, Sri Lanka.,Department of Physics and Astronomy, Georgia State University, Atlanta GA
| | - M M Henary
- Department of Chemistry, Georgia State University, Atlanta GA
| | - A G U Perera
- Department of Physics and Astronomy, Georgia State University, Atlanta GA
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8
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Owens EA, Huynh HT, Stroeva EM, Barman A, Ziabrev K, Paul A, Nguyen SV, Laramie M, Hamelberg D, Germann MW, Wilson WD, Henary M. Second Generation G-Quadruplex Stabilizing Trimethine Cyanines. Bioconjug Chem 2019; 30:2647-2663. [PMID: 31518105 DOI: 10.1021/acs.bioconjchem.9b00571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-Quadruplex DNA has been recognized as a highly appealing target for the development of new selective chemotherapeutics, which could result in markedly reduced toxicity toward normal cells. In particular, the cyanine dyes that bind selectively to G-quadruplex structures without targeting duplex DNA have attracted attention due to their high amenability to structural modifications that allows fine-tuning of their biomolecular interactions. We have previously reported pentamethine and symmetric trimethine cyanines designed to effectively bind G-quadruplexes through end stacking interactions. Herein, we are reporting a second generation of drug candidates, the asymmetric trimethine cyanines. These have been synthesized and evaluated for their quadruplex binding properties. Incorporating a benz[c,d]indolenine heterocyclic unit increased overall quadruplex binding, and elongating the alkyl length increases the quadruplex-to-duplex binding specificity.
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Affiliation(s)
- Eric A Owens
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Hang T Huynh
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | - Ekaterina M Stroeva
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | | | - Kostiantyn Ziabrev
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | | | | | | | - Donald Hamelberg
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Markus W Germann
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Department of Biology , Georgia State University , Petit Science Center, 100 Piedmont Ave. , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Maged Henary
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
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9
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Abstract
Guanine-rich nucleic acid sequences able to form four-stranded structures (G-quadruplexes, G4) play key cellular regulatory roles and are considered as promising drug targets for anticancer therapy. On the basis of the organization of their structural elements, G4 ligands can be divided into three major families: one, fused heteroaromatic polycyclic systems; two, macrocycles; three, modular aromatic compounds. The design of modular G4 ligands emerged as the answer to achieve not only more drug-like compounds but also more selective ligands by targeting the diversity of the G4 loops and grooves. The rationale behind the design of a very comprehensive set of ligands, with particular focus on the structural features required for binding to G4, is discussed and combined with the corresponding biochemical/biological data to highlight key structure-G4 interaction relationships. Analysis of the data suggests that the shape of the ligand is the major factor behind the G4 stabilizing effect of the ligands. The information here critically reviewed will certainly contribute to the development of new and better G4 ligands with application either as therapeutics or probes.
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Affiliation(s)
- Ana Rita Duarte
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Enrico Cadoni
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Ana S Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra Paulo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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10
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Gesevičius D, Neels A, Jenatsch S, Hack E, Viani L, Athanasopoulos S, Nüesch F, Heier J. Increasing Photovoltaic Performance of an Organic Cationic Chromophore by Anion Exchange. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018. [PMID: 29610723 DOI: 10.1001/advs.201700496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A symmetrical cyanine dye chromophore is modified with different counteranions to study the effect on crystal packing, polarizability, thermal stability, optical properties, light absorbing layer morphology, and organic photovoltaic (OPV) device parameters. Four sulfonate-based anions and the bulky bistriflylimide anion are introduced to the 2-[5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indolium chromophore using an Amberlyst A26 (OH- form) anion exchanger. Anionic charge distribution clearly correlates with device performance, whereby an average efficiency of 2% was reached in a standard bilayer organic solar. Evidence is given that the negative charge of the anion distributed over a large number of atoms is significantly more important than the size of the organic moieties of the sulfonate charge carrying group. This provides a clear strategy for future design of more efficient cyanine dyes for OPV applications.
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Affiliation(s)
- Donatas Gesevičius
- Laboratory for Functional Polymers Swiss Federal Laboratories for Materials Science and Technology, Empa Überlandstrasse 1298600 Dübendorf Switzerland
- Institute of Chemical Sciences and Engineering, ISIC Ecole Polytechnique Fédérale de Lausanne, EPFL Station 6CH-1015 Lausanne Switzerland
| | - Antonia Neels
- Center for X-ray AnalyticsSwiss Federal Laboratories for Materials Science and Technology, Empa Überlandstrasse 1298600 Dübendorf Switzerland
| | - Sandra Jenatsch
- Laboratory for Functional Polymers Swiss Federal Laboratories for Materials Science and Technology, Empa Überlandstrasse 1298600 Dübendorf Switzerland
| | - Erwin Hack
- Laboratory for Transport at Nanoscale Interfaces Swiss Federal Laboratories for Materials Science and Technology, Empa Überlandstrasse 1298600 Dübendorf Switzerland
| | - Lucas Viani
- Institute for Fluid Dynamics Nanoscience and Industrial Mathematics Universidad Carlos III de Madrid Avenida Universidad 3028911 Leganés Madrid Spain
| | - Stavros Athanasopoulos
- Departamento de Física Universidad Carlos III de Madrid Avenida Universidad 3028911 Leganés Madrid Spain
| | - Frank Nüesch
- Laboratory for Functional Polymers Swiss Federal Laboratories for Materials Science and Technology, Empa Überlandstrasse 1298600 Dübendorf Switzerland
- Institut des Matériaux Ecole Polytechnique Fédérale de Lausanne, EPFL Station 6CH-1015 Lausanne Switzerland
| | - Jakob Heier
- Laboratory for Functional Polymers Swiss Federal Laboratories for Materials Science and Technology, Empa Überlandstrasse 1298600 Dübendorf Switzerland
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11
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Gesevičius D, Neels A, Jenatsch S, Hack E, Viani L, Athanasopoulos S, Nüesch F, Heier J. Increasing Photovoltaic Performance of an Organic Cationic Chromophore by Anion Exchange. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1700496. [PMID: 29610723 PMCID: PMC5827648 DOI: 10.1002/advs.201700496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/09/2017] [Indexed: 05/06/2023]
Abstract
A symmetrical cyanine dye chromophore is modified with different counteranions to study the effect on crystal packing, polarizability, thermal stability, optical properties, light absorbing layer morphology, and organic photovoltaic (OPV) device parameters. Four sulfonate-based anions and the bulky bistriflylimide anion are introduced to the 2-[5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indolium chromophore using an Amberlyst A26 (OH- form) anion exchanger. Anionic charge distribution clearly correlates with device performance, whereby an average efficiency of 2% was reached in a standard bilayer organic solar. Evidence is given that the negative charge of the anion distributed over a large number of atoms is significantly more important than the size of the organic moieties of the sulfonate charge carrying group. This provides a clear strategy for future design of more efficient cyanine dyes for OPV applications.
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Affiliation(s)
- Donatas Gesevičius
- Laboratory for Functional PolymersSwiss Federal Laboratories for Materials Science and Technology, EmpaÜberlandstrasse 1298600DübendorfSwitzerland
- Institute of Chemical Sciences and Engineering, ISICEcole Polytechnique Fédérale de Lausanne, EPFLStation 6CH‐1015LausanneSwitzerland
| | - Antonia Neels
- Center for X‐ray AnalyticsSwiss Federal Laboratories for Materials Science and Technology, EmpaÜberlandstrasse 1298600DübendorfSwitzerland
| | - Sandra Jenatsch
- Laboratory for Functional PolymersSwiss Federal Laboratories for Materials Science and Technology, EmpaÜberlandstrasse 1298600DübendorfSwitzerland
| | - Erwin Hack
- Laboratory for Transport at Nanoscale InterfacesSwiss Federal Laboratories for Materials Science and Technology, EmpaÜberlandstrasse 1298600DübendorfSwitzerland
| | - Lucas Viani
- Institute for Fluid DynamicsNanoscience and Industrial MathematicsUniversidad Carlos III de MadridAvenida Universidad 3028911LeganésMadridSpain
| | - Stavros Athanasopoulos
- Departamento de FísicaUniversidad Carlos III de MadridAvenida Universidad 3028911LeganésMadridSpain
| | - Frank Nüesch
- Laboratory for Functional PolymersSwiss Federal Laboratories for Materials Science and Technology, EmpaÜberlandstrasse 1298600DübendorfSwitzerland
- Institut des MatériauxEcole Polytechnique Fédérale de Lausanne, EPFLStation 6CH‐1015LausanneSwitzerland
| | - Jakob Heier
- Laboratory for Functional PolymersSwiss Federal Laboratories for Materials Science and Technology, EmpaÜberlandstrasse 1298600DübendorfSwitzerland
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12
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Ihmels H, Mahmoud MM, Patrick BO. Optical differentiation between quadruplex DNA and duplex DNA with a [2.2.2]heptamethinecyanine dye. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Mohamed M.A. Mahmoud
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Brian O. Patrick
- Department of Chemistry; University of British Columbia; Vancouver Canada
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13
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Shershov VE, Kuznetsova VE, Lapa SA, Spitsyn MA, Guseinov TO, Tkachev YV, Zasedatelev AS, Chudinov AV. Synthesis and characterization of novel zwitterionic heptamethine indocyanine fluorophores. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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14
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Funke A, Weisz K. Comprehensive Thermodynamic Profiling for the Binding of a G-Quadruplex Selective Indoloquinoline. J Phys Chem B 2017; 121:5735-5743. [DOI: 10.1021/acs.jpcb.7b02686] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Andrea Funke
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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15
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Buchholz I, Karg B, Dickerhoff J, Sievers-Engler A, Lämmerhofer M, Weisz K. Selective Targeting of G-Quadruplex Structures by a Benzothiazole-Based Binding Motif. Chemistry 2017; 23:5814-5823. [PMID: 28276093 DOI: 10.1002/chem.201700298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 12/28/2022]
Abstract
A benzothiazole derivative was identified as potent ligand for DNA G-quadruplex structures. Fluorescence titrations revealed selective binding to quadruplexes of different topologies including parallel, antiparallel, and (3+1) hybrid structures. The parallel c-MYC sequence was found to constitute the preferred target with dissociation constants in the micromolar range. Binding of the benzothiazole-based ligand to c-MYC was structurally and thermodynamically characterized in detail by employing a comprehensive set of spectroscopic and calorimetric techniques. Job plot analyses and mass spectral data indicate noncooperative ligand binding to form complexes with 1:1 and 2:1 stoichiometries. Whereas stacking interactions are suggested by optical methods, NMR chemical shift perturbations also indicate significant rearrangements of both 5'- and 3'-flanking sequences upon ligand binding. Additional isothermal calorimetry studies yield a thermodynamic profile of the ligand-quadruplex association and reveal enthalpic contributions to be the major driving force for binding. Structural and thermodynamic information obtained in the present work provides the basis for the rational development of benzothiazole derivatives as promising quadruplex binding agents.
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Affiliation(s)
- Ina Buchholz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Adrian Sievers-Engler
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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16
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Lin D, Fei X, Gu Y, Wang C, Tang Y, Li R, Zhou J. A benzindole substituted carbazole cyanine dye: a novel targeting fluorescent probe for parallel c-myc G-quadruplexes. Analyst 2016; 140:5772-80. [PMID: 26176020 DOI: 10.1039/c5an00866b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Many organic ligands were synthesized to recognize G-quadruplexes. However, different kinds of G-quadruplexes (G4s) possess different structures and functions. Therefore, selective recognition of certain types of G4s is important for the study of G4s. In this paper, a novel cyanine dye, 3-(2-(4-vinylpyridine))-6-(2-((1-(4-sulfobutyl))-3,3-dimethyl-2-vinylbenz[e]indole)-9-ethyl-carbazole (9E PBIC), composed of benzindole and carbazole was designed and synthesised. The studies on UV-vis and fluorescence properties of the dye with different DNA forms showed that the dye exhibits almost no fluorescence under aqueous buffer conditions, but it increased over 100 fold in the presence of c-myc G4 and 10-30 fold in the presence of other G4s, while little in the presence of single/double-stranded DNA, indicating that it has excellent selectivity to c-myc 2345 G4. For the binding studies the dye is interacted with the c-myc 2345 G-quadruplex by using the end-stack binding model. It can be said that the dye is an excellent targeting fluorescent probe for c-myc G-quadruplexes.
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Affiliation(s)
- Dayong Lin
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.
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17
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Wu Q, Zheng K, Liao S, Ding Y, Li Y, Mei W. Arene Ruthenium(II) Complexes as Low-Toxicity Inhibitor against the Proliferation, Migration, and Invasion of MDA-MB-231 Cells through Binding and Stabilizing c-myc G-Quadruplex DNA. Organometallics 2016. [DOI: 10.1021/acs.organomet.5b00820] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Qiong Wu
- Key
Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China
| | - Kangdi Zheng
- School
of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Siyan Liao
- School
of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 510180, China
| | - Yang Ding
- School
of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yangqiu Li
- Key
Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China
| | - Wenjie Mei
- School
of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
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18
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Benz[c,d]indolium-containing Monomethine Cyanine Dyes: Synthesis and Photophysical Properties. Molecules 2015; 21:E23. [PMID: 26712725 PMCID: PMC6274575 DOI: 10.3390/molecules21010023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 01/24/2023] Open
Abstract
Asymmetric monomethine cyanines have been extensively used as probes for nucleic acids among other biological systems. Herein we report the synthesis of seven monomethine cyanine dyes that have been successfully prepared with various heterocyclic moieties such as quinoline, benzoxazole, benzothiazole, dimethyl indole, and benz[e]indole adjoining benz[c,d]indol-1-ium, which was found to directly influence their optical and energy profiles. In this study the optical properties vs. structural changes were investigated using nuclear magnetic resonance and computational approaches. The twisted conformation unique to monomethine cyanines was exploited in DNA binding studies where the newly designed sensor displayed an increase in fluorescence when bound in the DNA grooves compared to the unbound form.
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19
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Karg B, Funke A, Ficht A, Sievers-Engler A, Lämmerhofer M, Weisz K. Molecular Recognition and Visual Detection of G-Quadruplexes by a Dicarbocyanine Dye. Chemistry 2015; 21:13802-11. [DOI: 10.1002/chem.201502118] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Indexed: 11/12/2022]
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20
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Recent Developments in G-Quadruplex Probes. ACTA ACUST UNITED AC 2015; 22:812-28. [DOI: 10.1016/j.chembiol.2015.06.016] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 11/24/2022]
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21
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Mahoney DP, Owens EA, Fan C, Hsiang JC, Henary MM, Dickson RM. Tailoring cyanine dark states for improved optically modulated fluorescence recovery. J Phys Chem B 2015; 119:4637-43. [PMID: 25763888 DOI: 10.1021/acs.jpcb.5b00777] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cyanine dyes are well-known for their bright fluorescence and utility in biological imaging. However, cyanines also readily photoisomerize to produce nonemissive dark states. Co-illumination with a secondary, red-shifted light source on-resonance with the longer wavelength absorbing dark state reverses the photoisomerization and returns the cyanine dye to the fluorescent manifold, increasing steady-state fluorescence intensity. Modulation of this secondary light source dynamically alters emission intensity, drastically improving detection sensitivity and facilitating fluorescence signals to be recovered from an otherwise overwhelming background. Red and near-IR emitting cyanine derivatives have been synthesized with varying alkyl chain lengths and halogen substituents to alter dual-laser fluorescence enhancement. Photophysical properties and enhancement with dual laser modulation were coupled with density functional calculations to characterize substituent effects on dark state photophysics, potentially improving detection in high background biological environments.
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Affiliation(s)
| | - Eric A Owens
- ‡Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | | | | | - Maged M Henary
- ‡Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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22
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Hu H, Owens EA, Su H, Yan L, Levitz A, Zhao X, Henary M, Zheng YG. Exploration of cyanine compounds as selective inhibitors of protein arginine methyltransferases: synthesis and biological evaluation. J Med Chem 2015; 58:1228-43. [PMID: 25559100 PMCID: PMC4610307 DOI: 10.1021/jm501452j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Protein arginine methyltransferase
1 (PRMT1) is involved in many biological activities, such as gene
transcription, signal transduction, and RNA processing. Overexpression
of PRMT1 is related to cardiovascular diseases, kidney diseases, and
cancers; therefore, selective PRMT1 inhibitors serve as chemical probes
to investigate the biological function of PRMT1 and drug candidates
for disease treatment. Our previous work found trimethine cyanine
compounds that effectively inhibit PRMT1 activity. In our present
study, we systematically investigated the structure–activity
relationship of cyanine structures. A pentamethine compound, E-84
(compound 50), showed inhibition on PRMT1 at the micromolar
level and 6- to 25-fold selectivity over CARM1, PRMT5, and PRMT8.
The cellular activity suggests that compound 50 permeated
the cellular membrane, inhibited cellular PRMT1 activity, and blocked
leukemia cell proliferation. Additionally, our molecular docking study
suggested compound 50 might act by occupying the cofactor
binding site, which provided a roadmap to guide further optimization
of this lead compound.
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Affiliation(s)
- Hao Hu
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia , Athens, Georgia 30602, United States
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23
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Moreira BG, You Y, Owczarzy R. Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model. Biophys Chem 2015; 198:36-44. [PMID: 25645886 DOI: 10.1016/j.bpc.2015.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/02/2015] [Accepted: 01/02/2015] [Indexed: 12/25/2022]
Abstract
Cyanine dyes are important chemical modifications of oligonucleotides exhibiting intensive and stable fluorescence at visible light wavelengths. When Cy3 or Cy5 dye is attached to 5' end of a DNA duplex, the dye stacks on the terminal base pair and stabilizes the duplex. Using optical melting experiments, we have determined thermodynamic parameters that can predict the effects of the dyes on duplex stability quantitatively (ΔG°, Tm). Both Cy dyes enhance duplex formation by 1.2 kcal/mol on average, however, this Gibbs energy contribution is sequence-dependent. If the Cy5 is attached to a pyrimidine nucleotide of pyrimidine-purine base pair, the stabilization is larger compared to the attachment to a purine nucleotide. This is likely due to increased stacking interactions of the dye to the purine of the complementary strand. Dangling (unpaired) nucleotides at duplex terminus are also known to enhance duplex stability. Stabilization originated from the Cy dyes is significantly larger than the stabilization due to the presence of dangling nucleotides. If both the dangling base and Cy3 are present, their thermodynamic contributions are approximately additive. New thermodynamic parameters improve predictions of duplex folding, which will help design oligonucleotide sequences for biophysical, biological, engineering, and nanotechnology applications.
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Affiliation(s)
- Bernardo G Moreira
- Department of Molecular Genetics, Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - Yong You
- Department of Molecular Genetics, Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
| | - Richard Owczarzy
- Department of Molecular Genetics, Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA.
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24
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Yu L, Yang Q, Xiang J, Sun H, Wang L, Li Q, Guan A, Tang Y. Targeting of parallel c-myc G-quadruplex by dimeric cyanine dye supramolecular assembly: dependence on the linker length. Analyst 2015; 140:1637-46. [DOI: 10.1039/c4an01912a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recognizing ability of parallel c-myc G-quadruplex by dimeric cyanine dyes depends on their linker length.
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Affiliation(s)
- Lijia Yu
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Qianfan Yang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Junfeng Xiang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Lixia Wang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
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25
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Dzubiel D, Ihmels H, Mahmoud MMA, Thomas L. A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR). Beilstein J Org Chem 2014; 10:2963-74. [PMID: 25550763 PMCID: PMC4273293 DOI: 10.3762/bjoc.10.314] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/26/2014] [Indexed: 11/23/2022] Open
Abstract
The interactions of the ILPR sequence (ILPR = "insulin-linked polymorphic region") a2 [d(ACAG4TGTG4ACAG4TGTG4)] with [2.2.2]heptamethinecyanine derivatives 1a–e and with the already established quadruplex ligands coralyne (2), 3,3′-[2,6-pyridinediylbis(carbonylimino)]bis[1-methylquinolinium] (3), 4,4′,4′′,4′′′-(21H,23H-porphine-5,10,15,20-tetrayl)tetrakis[1-methylpyridinium] (4), naphtho[2,1-b:3,4-b′:6,5-b′′:7,8-b′′′]tetraquinolizinium (5) and thiazole orange (6) were studied. It is demonstrated with absorption, fluorescence and CD spectroscopy that all investigated ligands bind with relatively high affinity to the ILPR-quadruplex DNA a2 (0.2–5.5 × 106 M−1) and that in most cases the binding parameters of ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences.
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Affiliation(s)
- Darinka Dzubiel
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Mohamed M A Mahmoud
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Laura Thomas
- Department Chemie-Biologie, Universität Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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26
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Pisoni DS, Todeschini L, Borges ACA, Petzhold CL, Rodembusch FS, Campo LF. Symmetrical and asymmetrical cyanine dyes. Synthesis, spectral properties, and BSA association study. J Org Chem 2014; 79:5511-20. [PMID: 24845528 DOI: 10.1021/jo500657s] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
New cyanines were prepared by an efficient and practical route with satisfactory overall yield from low-cost starting materials. The photophysical behavior of the cyanines was investigated using UV-vis and steady-state fluorescence in solution, as well as their association with bovine serum albumin (BSA) in phosphate buffer solution (PBS). No cyanine aggregation was observed in organic solvents or in phosphate buffer solution. The alkyl chain length in the quaternized nitrogen was shown to be fundamental for BSA detection in PBS in these dyes.
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Affiliation(s)
- Diego S Pisoni
- Instituto de Quı́mica, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500, CP 15003. CEP 91501-970, Porto Alegre-RS, Brazil
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27
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2-{(E)-2-[(3E)-2-Chloro-3-{(2E)-2-[1,1-dimethyl-3-(3-phenylpropyl)-1,3-dihydro-2H-benzo[e]indol-2-ylidene]-ethylidene}cyclohex-1-en-1-yl]ethenyl}-1,1-dimethyl-3-(3-phenylpropyl)-1H-benzo[e]indolium Iodide. MOLBANK 2014. [DOI: 10.3390/m814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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28
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Hyun H, Owens EA, Narayana L, Wada H, Gravier J, Bao K, Frangioni JV, Choi HS, Henary M. Central C-C Bonding Increases Optical and Chemical Stability of NIR Fluorophores. RSC Adv 2014; 4:58762-58768. [PMID: 25530846 PMCID: PMC4267294 DOI: 10.1039/c4ra11225c] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Functional near-infrared (NIR) fluorophores have played a major role in the recent advances in bioimaging. However, the optical and physicochemical stabilities of NIR fluorophores in the biological and physiological environment are still a challenge. Especially, the ether linkage on the meso carbon of heptamethine core is fragile when exposed to serum proteins or other amine-rich biomolecules. To solve such a structural limitation, a rigid carbon-carbon bond was installed onto the framework of ether-linked NIR fluorophores through the Suzuki coupling. The robust fluorophores replaced as ZW800-1C and ZW800-3C displayed enhanced optical and chemical stability in various solvents and a 100% warm serum environment (> 99%, 24 h). The biodistribution and clearance of C-C coupled ZW800 compounds were almost identical to the previously developed oxygen-substituted ZW800 compounds. When conjugated with a small molecule ligand, ZW800-1C maintained the identical stable form in warm serum (>98%, 24 h), while ZW800-1A hydrolyzed quickly after 4 h incubation (34%, 24 h).
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Affiliation(s)
- Hoon Hyun
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
| | - Eric A. Owens
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 3030
| | - Lakshminarayana Narayana
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 3030
| | - Hideyuki Wada
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
| | - Julien Gravier
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
| | - Kai Bao
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
| | - John V. Frangioni
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
- Department of Radiology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
- Curadel, LLC, 377 Plantation Street, Worcester, MA 01605, USA
| | - Hak Soo Choi
- Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
| | - Maged Henary
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 3030
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29
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Castor KJ, Liu Z, Fakhoury J, Hancock MA, Mittermaier A, Moitessier N, Sleiman HF. A platinum(II) phenylphenanthroimidazole with an extended side-chain exhibits slow dissociation from a c-Kit G-quadruplex motif. Chemistry 2013; 19:17836-45. [PMID: 24249701 DOI: 10.1002/chem.201301590] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 09/16/2013] [Indexed: 01/05/2023]
Abstract
A series of three platinum(II) phenanthroimidazoles each containing a protonable side-chain appended from the phenyl moiety through copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) were evaluated for their capacities to bind to human telomere, c-Myc, and c-Kit derived G-quadruplexes. The side-chain has been optimized to enable a multivalent binding mode to G-quadruplex motifs, which would potentially result in selective targeting. Molecular modeling, high-throughput fluorescence intercalator displacement (HT-FID) assays, and surface plasmon resonance (SPR) studies demonstrate that complex 2 exhibits significantly slower dissociation rates compared to platinum phenanthroimidazoles without side-chains and other reported G-quadruplex binders. Complex 2 showed little cytotoxicity in HeLa and A172 cancer cell lines, consistent with the fact that it does not follow a telomere-targeting pathway. Preliminary mRNA analysis shows that 2 specifically interacts with the ckit promoter region. Overall, this study validates 2 as a useful molecular probe for c-Kit related cancer pathways.
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Affiliation(s)
- Katherine J Castor
- McGill University Department of Chemistry, 801 Sherbrooke West, Montreal, Quebec, H3A 0B8 (Canada)
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30
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Selective G-quadruplex DNA recognition by a new class of designed cyanines. Molecules 2013; 18:13588-607. [PMID: 24192912 PMCID: PMC4457452 DOI: 10.3390/molecules181113588] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/26/2013] [Accepted: 10/29/2013] [Indexed: 12/15/2022] Open
Abstract
A variety of cyanines provide versatile and sensitive agents acting as DNA stains and sensors and have been structurally modified to bind in the DNA minor groove in a sequence dependent manner. Similarly, we are developing a new set of cyanines that have been designed to achieve highly selective binding to DNA G-quadruplexes with much weaker binding to DNA duplexes. A systematic set of structurally analogous trimethine cyanines has been synthesized and evaluated for quadruplex targeting. The results reveal that elevated quadruplex binding and specificity are highly sensitive to the polymethine chain length, heterocyclic structure and intrinsic charge of the compound. Biophysical experiments show that the compounds display significant selectivity for quadruplex binding with a higher preference for parallel stranded quadruplexes, such as cMYC. NMR studies revealed the primary binding through an end-stacking mode and SPR studies showed the strongest compounds have primary KD values below 100 nM that are nearly 100-fold weaker for duplexes. The high selectivity of these newly designed trimethine cyanines for quadruplexes as well as their ability to discriminate between different quadruplexes are extremely promising features to develop them as novel probes for targeting quadruplexes in vivo.
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