Fluorescent Probes for Live Cell Thiol Detection
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Some New Nitrogen Bridgehead Heterocyclic Cyanine Dyes
Some New Nitrogen Bridgehead Heterocyclic Cyanine Dyes A. I. M. KORAIEM, H. A. SHINDY, and R. M. ABU EL-HAMD Department of Chemistry, Aswan Faculty of Science, Aswan, Egypt Received 21 July 1998 Accepted for publication 30 December 1999 New monomethine, trimethine, and azomethine cyanine dyes of pyrazolo^o'iSjôJÍpyrazinio/l^- oxa£Ínio)[2,3,4-ij']quinolin-ll-ium bromides were prepared. These cyanines were identified by ele mental and spectral analyses. The visible absorption spectra of some selected dyes were investigated in single and mixed solvents, and also in aqueous buffer solutions. The spectral shifts are discussed in relation to molecular structure and in terms of medium effects. Molecular complex formation with DMF was verified through mixed-solvent studies. As an extension to our earlier work on the syn Extra quaternization of the former intermediates thesis and studies of cyanine dyes [1—3], some new using an excess amount of ethyl iodide under con nitrogen bridgehead heterocyclic cyanine dye moi trolled conditions gave 9-ethyl-8-R-10-methylpyrazo- eties have been synthesized in view of the applica lo[4^5^5,6](pyrazinio/l,4-oxazinio) [2,3,4- zj']quinolin- bility of such compounds in production of photother- ll(9)-ium bromides iodides (IVa—IVe). Further re mographic imaging materials [4], electrophotographic action of the latter compounds with iV-methylpyridi- lithographic printing material for semiconductor laser nium, -quinolinium, resp. -isoquinolinium iodide in exposure [5], and as indicator and pH sensors [6], or volving active hydrogen atom in the position 11 or as antitumour agents [7]. 8 under piperidine catalysis gave the correspond Within these respects, pyrazolo[4',5':5,6](pyrazi- ing unsymmetrical bromides iodides of 9-ethyl-8-R- nio/1,4-oxazinio) [2,3,4- i,j\ quinolin-11-ium bromides pyrazolo[4^5^5,6](pyrazinio/l,4-oxazinio) [2,3,4- i,j]- Ilia—IIIc were used as key intermediates for the dye quinolin-ll-ium-10[4(l)]-monomethine cyanine dyes synthesis. -
Cyanine Dye–Nucleic Acid Interactions
Top Heterocycl Chem (2008) 14: 11–29 DOI 10.1007/7081_2007_109 © Springer-Verlag Berlin Heidelberg Published online: 23 February 2008 Cyanine Dye–Nucleic Acid Interactions Bruce A. Armitage Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA [email protected] 1Introduction................................... 12 2 Symmetrical Cyanines ............................. 14 2.1 NoncovalentBinding.............................. 14 2.2 CovalentBinding................................ 16 3 Unsymmetrical Cyanines ............................ 17 3.1 NoncovalentBinding.............................. 17 3.1.1InsightsintoPhotophysics........................... 17 3.1.2NewUnsymmetricalDyes............................ 18 3.1.3Applications................................... 21 3.2 CovalentBinding................................ 23 3.2.1DNA-ConjugatedDyes............................. 24 3.2.2PNA-ConjugatedDyes.............................. 25 3.2.3Peptide-andProtein-ConjugatedDyes.................... 26 4Conclusions................................... 27 References ....................................... 28 Abstract Cyanine dyes are widely used in biotechnology due to their ability to form fluor- escent complexes with nucleic acids. This chapter describes how the structure of the dye determines the mode in which it binds to nucleic acids as well as the fluorescence prop- erties of the resulting complexes. Related dyes, such as hemicyanines and styryl dyes, are briefly described as well. In addition, covalent conjugates -
Synthesis of Near-Infrared Heptamethine Cyanine Dyes
Georgia State University ScholarWorks @ Georgia State University Chemistry Theses Department of Chemistry 4-26-2010 Synthesis of Near-Infrared Heptamethine Cyanine Dyes Jamie Loretta Gragg Georgia State University, [email protected] Follow this and additional works at: https://scholarworks.gsu.edu/chemistry_theses Recommended Citation Gragg, Jamie Loretta, "Synthesis of Near-Infrared Heptamethine Cyanine Dyes." Thesis, Georgia State University, 2010. https://scholarworks.gsu.edu/chemistry_theses/28 This Thesis is brought to you for free and open access by the Department of Chemistry at ScholarWorks @ Georgia State University. It has been accepted for inclusion in Chemistry Theses by an authorized administrator of ScholarWorks @ Georgia State University. For more information, please contact [email protected]. SYNTHESIS OF NEAR-INFRARED HEPTAMETHINE CYANINE DYES by JAMIE L. GRAGG Under the Direction of Dr. Maged M. Henary ABSTRACT Carbocyanine dyes are organic compounds containing chains of conjugated methine groups with electron-donating and electron-withdrawing substituents at the terminal 1 2 + - heterocycles of the general formula [R -(CH)n-R ] X . The synthetic methodology and optical properties of carbocyanines will be discussed. This thesis consists of two parts: (A) synthesis and optical properties of novel carbocyanine dyes substituted with various amines and the synthesis of unsymmetrical carbocyanine dyes containing monofunctional groups for bioconjugation. (B) synthesis of heptamethine carbocyanine dyes to be used for image-guided surgery. ii In part A, the synthesis of carbocyanine dyes functionalized with various amines and studies of their optical properties with respect to absorbance, fluorescence, quantum yield and extinction coefficient will be presented. These property studies will aid in designing efficient dyes for future biomedical applications. -
Two-Photon Excited Photoconversion of Cyanine-Based Dyes
Two-photon excited photoconversion of cyanine-based dyes The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Kwok, Sheldon J. J. et al. “Two-Photon Excited Photoconversion of Cyanine-Based Dyes.” Scientific Reports 6 (2016): 23866. © 2016 Macmillan Publishers Limited As Published http://dx.doi.org/10.1038/srep23866 Publisher Nature Publishing Group Version Final published version Citable link http://hdl.handle.net/1721.1/108348 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/4.0/ www.nature.com/scientificreports OPEN Two-photon excited photoconversion of cyanine-based dyes Sheldon J. J. Kwok1,2,*, Myunghwan Choi1,3,*, Brijesh Bhayana1, Xueli Zhang4,5, Chongzhao Ran4 & Seok-Hyun Yun1,2 Received: 14 October 2015 The advent of phototransformable fluorescent proteins has led to significant advances in optical Accepted: 15 March 2016 imaging, including the unambiguous tracking of cells over large spatiotemporal scales. However, these Published: 31 March 2016 proteins typically require activating light in the UV-blue spectrum, which limits their in vivo applicability due to poor light penetration and associated phototoxicity on cells and tissue. We report that cyanine- based, organic dyes can be efficiently photoconverted by nonlinear excitation at the near infrared (NIR) window. Photoconversion likely involves singlet-oxygen mediated photochemical cleavage, yielding blue-shifted fluorescent products. Using SYTO62, a biocompatible and cell-permeable dye, we demonstrate photoconversion in a variety of cell lines, including depth-resolved labeling of cells in 3D culture. Two-photon photoconversion of cyanine-based dyes offer several advantages over existing photoconvertible proteins, including use of minimally toxic NIR light, labeling without need for genetic intervention, rapid kinetics, remote subsurface targeting, and long persistence of photoconverted signal. -
Water-Soluble Pyrrolopyrrole Cyanine (Ppcy) NIR Fluorophores† Cite This: Chem
Erschienen in: Chemical Communications ; 2014, 50. - S. 4755-4758 ChemComm View Article Online COMMUNICATION View Journal | View Issue Water-soluble pyrrolopyrrole cyanine (PPCy) NIR fluorophores† Cite this: Chem. Commun., 2014, 50, 4755 Simon Wiktorowski, Christelle Rosazza, Martin J. Winterhalder, Ewald Daltrozzo Received 7th February 2014, and Andreas Zumbusch* Accepted 21st March 2014 DOI: 10.1039/c4cc01014k www.rsc.org/chemcomm Water-soluble derivatives of pyrrolopyrrole cyanines (PPCys) have been dyes, BODIPYs or others.7 Notable are also advances in other fields, synthesized by a post-synthetic modification route. In highly polar like the engineering of GFP-related fluorescing proteins or quantum media, these dyes are excellent NIR fluorophores. Labeling experiments dots, which have resulted in the synthesis of novel systems with NIR show how these novel dyes are internalized into mammalian cells. emission.8 To date, however, only a few water-soluble dyes with strong NIR absorptions and emissions have been known. Apart from the Near-infrared (NIR) light absorbing and emitting compounds have general scarcity of NIR absorbing molecules, the main reason for this attracted a lot of interest since the 1990’s.1 Initially, this was motivated is that NIR absorption is commonly observed in extended p-systems by their use in optical data storage or as laser dyes. Recently, however, which most often are hydrophobic. The incorporation of hydrophilic new applications of NIR dyes have emerged, which has led to a surge of functionalities into -
Chiral Indole Intermediates and Their Fluorescent
(19) TZZ_ _T (11) EP 1 525 265 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C09B 23/02 (2006.01) G01N 33/58 (2006.01) 20.07.2011 Bulletin 2011/29 G01N 33/533 (2006.01) C12Q 1/00 (2006.01) C07D 491/22 (2006.01) C07D 403/06 (2006.01) (21) Application number: 03808367.1 (86) International application number: (22) Date of filing: 09.05.2003 PCT/US2003/014632 (87) International publication number: WO 2004/039894 (13.05.2004 Gazette 2004/20) (54) CHIRAL INDOLE INTERMEDIATES AND THEIR FLUORESCENT CYANINE DYES CONTAINING FUNCTIONAL GROUPS CHIRALE INDOLE ALS ZWISCHENPRODUKTE UND DARAUS HERGESTELLTE CYANINFLUORESZENZFARBSTOFFE MIT FUNKTIONELLEN GRUPPEN INTERMEDIAIRES CHIRAUX D’INDOLE ET LEURS COLORANTS DE CYANINE FLUORESCENTS CONTENANT DES GROUPES FONCTIONNELS (84) Designated Contracting States: • WEST, Richard Martin, AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Amersham Biosciences UK Ltd. HU IE IT LI LU MC NL PT RO SE SI SK TR Buckinghamshire HP7 9NA (GB) (30) Priority: 10.05.2002 US 379107 P (74) Representative: Franks, Barry Gerard et al GE Healthcare Limited (43) Date of publication of application: Amersham Place 27.04.2005 Bulletin 2005/17 Little Chalfont Buckinghamshire HP7 9NA (GB) (60) Divisional application: 10178959.2 / 2 258 776 (56) References cited: WO-A-02/26891 US-A- 5 268 486 (73) Proprietors: US-A- 6 133 445 US-A- 6 133 445 • CARNEGIE MELLON UNIVERSITY US-B1- 6 180 087 Pittsburgh, Pennsylvania 15213 (US) • GE Healthcare Limited Remarks: Little Chalfont Thefilecontainstechnicalinformationsubmittedafter Buckinghamshire HP7 9NA (GB) the application was filed and not included in this specification (72) Inventors: • MUJUMDAR, Ratnaker, B. -
Reactive Intermediates in Naquotinib Metabolism
RSC Advances View Article Online PAPER View Journal | View Issue Reactive intermediates in naquotinib metabolism identified by liquid chromatography-tandem mass Cite this: RSC Adv.,2019,9,10211 spectrometry: phase I metabolic profiling Mohamed W. Attwa, ab Adnan A. Kadi,a Haitham AlRabiaha and Hany W. Darwish*ac Tyrosine kinase inhibitors (TKIs) are very efficient for the treatment of EGFR-mutated lung cancer and show improved therapeutic efficacy. However, treatment with both first- and second-generation TKIs results in acquired resistance and is related to various toxicities; the EGFR T790M mutation has been associated with this resistance. Naquotinib (ASP8273, NQT) is a novel third-generation epidermal growth factor receptor tyrosine kinase inhibitor that has been shown to be more potent than osimertinib in the management of L858R plus T790M mutations. However, its bioactivation may occur and promote the formation of reactive electrophiles that are toxic. We hypothesize that these reactive intermediates are potentially involved in the side effects of NQT. Reactive metabolites are often formed by phase I metabolic Creative Commons Attribution 3.0 Unported Licence. reactions and cannot be characterized directly as they are transient in nature. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we screened for in vitro metabolites of NQT formed during incubation with human liver microsomes and evaluated the generation of reactive electrophiles using capturing agents, such as methoxyamine and potassium cyanide, as nucleophiles that form stable adducts for identification by LC-MS/MS. Eight NQT phase I metabolites were found that had been formed by N-demethylation, oxidation, hydroxylation, and reduction. In addition, three reactive Received 10th January 2019 electrophiles, two aldehydes, and one iminium ion were identified, and the corresponding bioactivation Accepted 24th March 2019 mechanisms were proposed. -
Chirality Transfer in 5-Exo Cyclizations of Axially Chiral O-Iodoanilides
CHIRALITY TRANSFER IN 5-EXO CYCLIZATIONS OF AXIALLY CHIRAL O-IODOANILIDES by Andre J. B. Lapierre B. Sc., McMaster University, 2000 Submitted to the Graduate Faculty of Arts and Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2005 UNIVERSITY OF PITTSBURGH FACULTY OF ARTS AND SCIENCES This dissertation was presented by Andre J. B. Lapierre It was defended on December 6th, 2005 and approved by Dr. Kay Brummond Dr. Theodore Cohen Dr. Michael Mokotoff Dr. Dennis Curran Dissertation Director ii To my wife and family, iii CHIRALITY TRANSFER IN 5-EXO CYCLIZATIONS OF AXIALLY CHIRAL O-IODOANILIDES Andre J. B. Lapierre, Ph.D. University of Pittsburgh, 2005 Stereoselective 5-exo radical and Heck cyclizations of axially chiral o-iodoanilides to enantioenriched oxindoles and dihydroindolones are described. Mechanisms for the transfer of chirality from the atropisomeric anilides to the newly formed stereocenters in the cyclic products are proposed and supported with physical data. Additionally, the N-aryl bond rotation barriers for eight o-iodoanilides are reported. A series of axially chiral N-allyl-o-iodoanilides were cyclized under room temperature radical conditions to dihydroindolones with good to excellent chirality transfer (74–97 %). Cyclization rate constant data is presented to rationalize the regioselective preference for N-allyl over N- acryloyl cyclization when an o-methyl group is present. X-ray crystallography was used to assign absolute configurations to a cyclization precursor/product pair. Radical 5-exo cyclizations of axially chiral o-iodoanilides bearing branched, bulky N-substituents are covered. The bulkiness of N-substituents permitted the resolution of a series of novel o-iodoanilides lacking a second ortho substituent. -
Glycolipids from Candida Bombicola: Polymerization of a 6-O-Acryloyl Sophorolipid Derivative
6208 Macromolecules 2000, 33, 6208-6210 Glycolipids from Candida bombicola: Polymerization of a 6-O-Acryloyl Sophorolipid Derivative Kirpal S. Bisht,† Wei Gao, and Richard A. Gross* Polytechnic University, NSF Center for Biocatalysis and Bioengineering, Six Metrotech Center, Brooklyn, New York 11201 Received January 31, 2000 Revised Manuscript Received May 25, 2000 Polymers with amphiphilic properties are of great Figure 1. Sophorolipids produced by Turolopsis bombicola interest since they are important components of a wide when grown on a mixture of glucose and oleic acid. range of industrial and pharmaceutical products.1 The modification of naturally occurring polysaccharides, was synthesized by refluxing the sophorolipid mixture which has been practiced for over a century, is a viable with an alcoholic solution of sodium methoxide.8 The route to amphiphilic glycolipid containing polymers. sophorolipid methyl ester was then subjected to acry- However, in view of the complex nature of polysaccha- loylation with vinyl acrylate (g2 equiv) in dry THF. The rides, their regioselective modification to form well- ability of the lipases PPL, CCL, PS-30, AK, MAP-10, defined products is tedious and is generally practiced Novozym-435, and Lipozyme IM to catalyze this trans- only as an academic curiosity. Incorporation of sugars formation was studied.9 Of the lipases evaluated, No- in synthetic polymers is a viable alternative for the vozym-435 was found to be the preferred catalyst. generation of amphiphilic polymers.2 However, selectiv- Acryloylation with an excess of vinyl acrylate (vinyl ity in such reactions often requires complex multistep acrylate:sophorolipid methyl ester g2:1) using No- synthetic pathways.3 Enzyme-catalyzed transformations vozym-435 as the catalyst gave 6′,6′′-diacryloylate as the can provide high selectivity. -
Orientation of Cyanine Fluorophores Terminally Attached to DNA Via Long, Flexible Tethers
1148 Biophysical Journal Volume 101 September 2011 1148–1154 Orientation of Cyanine Fluorophores Terminally Attached to DNA via Long, Flexible Tethers Jonathan Ouellet, Stephanie Schorr, Asif Iqbal, Timothy J. Wilson, and David M. J. Lilley* Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom ABSTRACT Cyanine fluorophores are commonly used in single-molecule FRET experiments with nucleic acids. We have previously shown that indocarbocyanine fluorophores attached to the 50-termini of DNA and RNA via three-carbon atom linkers stack on the ends of the helix, orienting their transition moments. We now investigate the orientation of sulfoindocarbocyanine fluorophores tethered to the 50-termini of DNA via 13-atom linkers. Fluorescence lifetime measurements of sulfoindocarbocya- nine 3 attached to double-stranded DNA indicate that the fluorophore is extensively stacked onto the terminal basepair at 15C, with properties that depend on the terminal sequence. In single molecules of duplex DNA, FRET efficiency between sulfoindo- carbocyanine 3 and 5 attached in this manner is modulated with helix length, indicative of fluorophore orientation and consistent with stacked fluorophores that can undergo lateral motion. We conclude that terminal stacking is an intrinsic property of the cyanine fluorophores irrespective of the length of the tether and the presence or absence of sulfonyl groups. However, compared to short-tether indocarbocyanine, the mean rotational relationship between the two fluorophores is changed by ~60 for the long- tether sulfoindocarbocyanine fluorophores. This is consistent with the transition moments becoming approximately aligned with the long axis of the terminal basepair for the long-linker species. -
USE and ASSESSMENT of MARKER DYES USED with HERBICIDES
SERA TR 96-21-07-03b USE and ASSESSMENT OF MARKER DYES USED WITH HERBICIDES Submitted to: Leslie Rubin, COTR Animal and Plant Health Inspection Service (APHIS) Policy and Program Development Environmental Analysis and Documentation United States Department of Agriculture Suite 5A44, Unit 149 4700 River Road Riverdale, MD 20737 Task No. 10 USDA Order Nos. 43-3187-7-0408 USDA Contract No. 53-3187-5-12 Submitted by: Syracuse Environmental Research Associates, Inc. 5100 Highbridge St., 42C Fayetteville, New York 13066-0950 Telephone: (315) 637-9560 Fax: (315) 637-0445 Internet: [email protected] December 21, 1997 USE and ASSESSMENT OF MARKER DYES USED WITH HERBICIDES Prepared by: Michelle Pepling1, Phillip H. Howard1, Patrick R. Durkin2, 1Syracuse Research Corporation 6225 Running Ridge Road North Syracuse, New York 13212-2509 2Syracuse Environmental Research Associates, Inc. 5100 Highbridge St., Building 42C Fayetteville, New York 13066-0950 Submitted to: Leslie Rubin, COTR Animal and Plant Health Inspection Service (APHIS) Policy and Program Development Environmental Analysis and Documentation United States Department of Agriculture Suite 5A44, Unit 149 4700 River Road Riverdale, MD 20737 Task No. 10 USDA Order Nos. 43-3187-7-0408 USDA Contract No. 53-3187-5-12 Submitted by: Syracuse Environmental Research Associates, Inc. 5100 Highbridge St., 42C Fayetteville, New York 13066-0950 Telephone: (315) 637-9560 Fax: (315) 637-0445 Internet: [email protected] December 21, 1997 TABLE OF CONTENTS TABLE OF CONTENTS .....................................................ii ACRONYMS, ABBREVIATIONS, AND SYMBOLS .............................. iii 1. INTRODUCTION .....................................................1 2. CURRENT PRACTICE .................................................2 3. GENERAL CONSIDERATIONS .........................................3 3.1. DEFINITIONS .................................................3 3.2. CLASSES OF DYES .............................................4 3.3. -
Array-Cgh Workshop Protocol 04/22/2015
ARRAY-CGH WORKSHOP PROTOCOL 04/22/2015 Array-based comparative genomic hybridization (aCGH) uses a two-color process to measure DNA copy number changes and copy-neutral Loss of Heterozygosity (LOH) or Uniparental Disomy (UPD)† in an experimental sample relative to a reference (control) sample. The process involves isolating high molecular weight genomic DNA, labeling the DNA with Cyanine- 3 or Cyanine-5 (Cy3 or Cy5) fluorophores, hybridizing labeled target to a DNA microarray, scanning, and data analysis. There are different vendors/protocols available for aCGH, but the general workflow is the same. DNA MICROARRAY: A fixed surface (typically glass) to which nucleic acids are immobilized. Depending on the application, DNA microarrays may be comprised of cDNA clones, BAC clones, oligonucleotides, PCR products or other materials. This workshop will utilize 60-mer oligonucleotides. PROBE: The nucleic acid attached to the microarray that is used to bind regions of genomic DNA in the samples. Probes are selected to be unique in the genome based on bioinformatics. Probe density and coverage determine, in part, the resolution of the DNA microarray. TARGET: This refers to the sample or control genomic DNA after it has been labeled with a fluorescent dye. The target is hybridized with the DNA microarray and binds, by complementary base pairing, with the probes on the array. † LOH and UPD detection only possible when using microarrays with single nucleotide polymorphism (SNP) probes and a control sample of known genotype. For Research Use Only. Not for Use in Diagnostic Procedures STEP 1: RESTRICTION DIGESTION: The purpose of this step is to fragment the high molecular weight genomic DNA (gDNA) into smaller pieces.