DY-635 and DY-704 as molecular pilots for cell-type specific delivery of siRNAs

Press A.T., Traeger A., Pietsch C., Mosig A., Wagner M., Clemens M.G., Jbeily N., Koch N., Gottschaldt M., Beziere N., Ermolayev V., Ntiachristos V., Popp J., Kessels M.M., Qualmann B., Schubert U.S., Bauer M., Cell type-specific delvery of short interfering RNAs by dye-functionalised theranostic nanoparticles, Nature Communications 5 (2014), Article Number: 5565 I doi:10.

Recent papers concerning in vivo-applications of DY-dyes

Busch, C., Passon, M., Wenzel, M., Socher, I., Kaiser, W. A. and Hilger, I. 2011. Detection of Leukotriene Receptor CysLT(1)R in Inflammatory Diseases by Molecular Imaging with Near-Infrared Fluorescence-Based Contrast Agents, Molecular Imaging 10 (2): 81-90

Busch, C., Schroter, T., Grabolle, M., Wenzel, M., Kempe, H., Kaiser, W. A., Resch-Genger, U. and Hilger, I. 2012. An In Vivo Spectral Multiplexing Approach for the Cooperative Imaging of Different Disease-Related Biomarkers with Near-Infrared Fluorescent Forster Resonance Energy Transfer Probes, Journal of Nuclear Medicine 53 (4): 638-646

Hamann, F. M., Brehm, R., Pauli, J., Grabolle, M., Frank, W., Kaiser, W. A., Fischer, D., Rech-Genger, U. and Hilger, I. 2011. Controlled Modulation of Serum Protein Binding and Biodistribution of Asymmetric Cyanine Dyes by Variation of the Number of Sulfonate Groups, Molecular Imaging 10 (4): 258-269

Laabs, E., Béhé, M., Kossatz, S., Frank, W., Kaiser, W. A. and Hilger, I. 2011. Optical Imaging of CCK2/Gastrin Receptor-Positive Tumors With a Minigastrin Near-Infrared Probe, Investigative Radiology 46 (3): 196-201

Pauli, J., Brehm, R., Spieles, M., Kaiser, W. A., Hilger, I. and Resch-Genger, U. 2010. Novel Fluorophores as Building Blocks for Optical Probes for In Vivo Near Infrared Fluorescence (NIRF) Imaging, J Fluoresc 20: 681-693

Pauli, U., Grabolle, M., Brehm, R., Spieles, M., Hamann, F. M., Wenzel, M., Hilger, I. and Resch-Genger, U. 2011. Suitable Labels for Molecular Imaging  Influence of Dye Structure and Hydrophilicity on the Spectroscopic Properties of IgG Conjugates, Bioconjugate Chem. 22: 1298-1308

DY-681 and DY-781 labeled primers

Ritz C.M., Wisseman V., Microsatellite Analyses of Artificial and Spontaneous Dogrose Hybrids Reveal the Hybridogenic Origin of Rosa micrantha by the Contribution of Unreduced Gametes, Journal of Heredity, doi:10.1093/jhered/esq124.

Review

Napp J., Mathejczyk J.E., Alves F., Optical imaging in vivo with a focus on paediatric disease:technical progress, current preclinical and clinical applications and future perspectives, Pediatr Radiol, (2011)DOI 10.1007/s00247-010-1907-0.

DY-682-labeled secondary antibodies

Koplin A., Preissler S., Ilina Y., Koch M., Scior A., Erhardt M., Deuerling E., A dual function for chaperones SSB-RAC and the NAC nascent polypeptide-associated complex on ribosomes, The Journal of Cell Biology, Vol. 189(2010)57-68.

DY-682 and DY-800 labeled secondary antibodies

Ferreira D.N., Katayama I.A., Oliveira I.B, Rosa K.T., Furukawa L.N.S., Coelho M.S., Casarini D.E., Heimann J.C., Salt-Induced Cardiac Hypertrophy and Interstitial Fibrosis Are Due to a Blood Pressure-Independent Mechanism in Wistar Rats, The Journal of Nutrition, 140(2010)1742-51.

DY-601XL, DY-613, V07-04118 and V07-04146 as stains in acid media

Brockmann S., Arnold T., Schweder Bt. Bernhard G., Visualizing Acidophilic Microorganisms in Biofilm Cummunities Using Acid Stable Fluorescence Dyes, Journal of Fluorescence, 20(2010)943-51.

DY-520XL in TIRF microscopy

Spendier K., Carroll-Portillo A., Lidke K.A., Wilson B.S., Timlin J.A., Thomas J.L., Distribution and Dynamics of Rat Basophilic Leukemia Immunoglobulin E Receptors (Fc3RI) on Planar Ligand-Presenting Surfaces, Biophysical Journal, 99(2010)388-397

DY-549 and DY-649 on protein microarrays

Schröder C., Jacob A., Tonack S., Radon T.P., Sill M., Zucknick M., Rüffer S., Costello E., Neoptolemos J.P., Crnogorac-Jurcevic T., Bauer A., Fellenberg K., Hoheisel J.D., Dual-color Proteomic Profiling of Complex Samples with a Microarray of 810 Cancer-related Antibodies, Mol Cell Proteomics. 9(2010)1271-1280.

Review

Paganin-Gioanni A., Bellard E., Paquereau L., Ecochard V., Golzio M., Teissié J., Fluorescence imaging agents in cancerology, Radiol Oncol 2010; 44(3): 142-148.

DY-520XL in multicolour microscopy

Carroll-Portillo A., Spendier K.,  Pfeiffer J., Griffiths G., Li H., Lidke K.A., Oliver J.M., Lidke D.S., Thomas J.L., Wilson B.S., Timlin J.A., Formation of a Mast Cell Synapse: FcRI Membrane Dynamics upon Binding Mobile or Immobilized Ligands on Surfaces, The Journal of Immunology, 184(2010)1328-1338.

DY-752 as imaging agent

Pöschinger T., Janunts E., Brünner H., Langenbucher A., CCD-based projectional imaging of fluorescent probes in tissue-like media: experimental setup and characterization, Zeitschrift für Medizinische Physik, 2010, in press.

DY-481XL and DYQ-661 as FRET-pair

Tan C., Gajovic-Eichelmann N., Stöcklein W.F.M., Polzius R., Bier F.F., Direct detection of 9-tetrahydrocannabinol in saliva using a novel homogeneous competitive immunoassay with fluorescence quenching, Analytica Chimica Acta, 658(2010)187-192.

DY-636 on labeled particles

Jiang X., Weise1 S., Hafner M., Röcker C., Zhang F., Parak W.J., Nienhaus G.U., Quantitative analysis of the protein corona on FePt nanoparticles formed by transferrin binding, J. R. Soc. Interface 6 February 2010 vol. 7 no. Suppl 1 S5-S13.

DY-682 in tumor imaging

Gong H., Kovar J., Little G., Chen H., Olive D.M., In Vivo Imaging of Xenograft Tumors Using an Epidermal Growth Factor Receptor-Specific Affibody Molecule Labeled with a Near-infrared Fluorophore, Neoplasia. 2010 February; 12(2): 139-149.

DY-681-labeled primers

Perovic D., Förster J., Devaux P., Hariri D., Guilleroux M., Kanyuka K., Lyons R., Weyen J., Feuerhelm D., Kastirr U., Sourdille P., Röder M., Ordon F., Mapping and diagnostic marker development for Soil-borne cereal mosaic virus resistance in bread wheat, Mol Breeding, 23(2009)641-653.

DY-681-UTP

Owczarek-Lipska M., Dolf G., Guziewicz K.E., Leeb T., Schelling C., Posthaus H. Braunschweig M.H., Bovine cardiac troponin I gene (TNNI3) as a candidate gene for bovine dilated cardiomyopathy, Archiv Tierzucht, 52(2009)113-123.

DY-781-dUTP in PCR application

Braunschweig M.H., Quantification of global DNA methylation with infrared fluorescence in liver and muscle tissues of differentially fed boars, Luminescence, 24(2009)213-216.

DY-633-HaloTag

Kosaka N., Ogawa M., Choyke P.L., Karassina N., Corona C., McDougall M., Lynch D., Hoyt C., Levenson R., Los G.V.,Kobayashi H., In Vivo Stable Tumor-Specific Painting in Various Colors Using Dehalogenase-Based Protein-Tag Fluorescent Ligands, Bioconjug Chem., 20(2009)1367-1374.

DY-681 in PCR application

Vollmer T., Kleesiek K., Dreier J., Lipopolysaccharide-binding protein (LBP) gene polymorphisms: Rapid genotyping by real-time PCR and association with infective endocarditis, Clinical Biochemistry 42 (2009) 1413-1419.

DY-750 and DY-776 in tumor imaging

Makino A., Kizaka-Kondoh S., Yamahara R., Hara I., Kanzaki T., Ozeki E., Hiraoka M., Kimura S., Near-infrared fluorescence tumor imaging using nanocarrier composed of poly(L-lactic acid)-block-poly(sarcosine) amphiphilic polydepsipeptide, Biomaterials, 30(2009)5156-5160

DY-485XL labeled secondary antibody

Vag T., Schramm T., Kaiser W.A., Hilger I., Proliferating and quiescent human umbilical vein endothelial cells (HUVECs): a potential in vitro model to evaluate contrast agents for molecular imaging of angiogenesis, Contrast Media & Molecular Imaging, 4(2009)192-198.

DY-615 in labeled peptides

Pola R., Studenovsky M., Pechar M., Ulbrich K., Hovorka O., Vetvicka D., Rihova B., HPMA-copolymer conjugates targeted to tumor endothelium using synthetic oligopeptides, Journal of Drug Targeting, 2009.

MegaStokes dyes in silica particles

Herz E., Burns A., Bonner D., Wiesner U., Large Stokes-Shift Fluorescent Silica Nanoparticles with ENhanced Emission Over Free Dye for Single Excitation Multiplexing, Macromolecular Rapid Communications, 30(2009)1907-10.

DY-635 and DY-647-biotin conjugates

Luschtinetz F., Dosche C., Kumke M.U., Influence of Streptavidin on the Absorption and Fluorescence Properties of Cyanine Dyes, Bioconjugate Chemistry, 20(2009)576-582.

DY-676, DY-681, DY-731, DY-751 and DY-776 for molecular imaging

Pauli J., Vag T., Haag R., Spieles M., Wenzel M., Kaiser W.A., Resch-Genger U., Hilger I., An in vitro characterization study of new near infrared dyes for molecular imaging, European Journal of Medicinal Chemistry, 44(2009)3496-3503.

DY-730, DY-731, DY-732, DY-734 and DY-780 in silica nanoparticles

Herz E., Ow H., Bonner D., Burns A., Wiesner U., Dye structure-optical property correlations in near-infrared fluorescent core-shell silica nanoparticles, Journal of Materials Chemistry, DOI:10/1039/b902286d.

V03-01136 (now FatRed) as fat stain

Heilig A., Göggerle A., Hinrichs J., Multiphase visualisation of fat containing beta-lactoglobulin-k-carrageenan gels by confocal scanning laser microscopy, using a novel dye, V03-01136, for fat staining, LWT - Food Science and Technology, 42(2009)646-53.

DY-547 in antibody labeling

Mindt T.L., Jungi V., Wyss S., Friedli A., Pla G., Novak-Hofer I., Grünberg J., Schibli R., Modification of Different IgG1 Antibodies via Glutamine and Lysine using Bacterial and Human Tissue Transglutaminase, Bioconjugate Chem., 19(2008)271-278.

DY-649 labeled antibodies

Almeida R.S., Brunke S., Albrecht A., Thewes S., Laue M., Edwards J.E.Jr., Filler S.G., Hube B., The Hyphal-Associated Adhesin and Invasin Als3 of Candida albicans Mediates Iron Acquisition from Host Ferritin, PLoS Pathogens, 4(2008)e1000217.

DY-675 for cancer imaging

Tanisaka H., Kizaka-Kondoh S., Makino A., Tanaka S., Hiraoka M., Kimura S., Near-Infrared Fluorescent Labeled Peptosome for Application to Cancer Imaging, Bioconjugate Chemistry, 19(2008)109-117.

DY-485XL in STED-microscopy

Schmidt R., Wurm C.A., Jakobs S., Engelhardt J., Egner A., Hell S.W., Spherical nanosized spot unravels the interior of cells, nature methods, 5(2008)539-544.

DY-548 and DY-648 on cDNA-microarrays

Maier M., Wutzler S., Bauer M., Trendafilov P., Henrich D., Marzi I., ALTERED GENE EXPRESSION PATTERNS IN DENDRITIC CELLS AFTER SEVERE TRAUMA: IMPLICATIONS FOR SYSTEMIC INFLAMMATION AND ORGAN INJURY, SHOCK, 30(2008)344-351.

DY-676 for in vivo imaging

Deissler V., Rüger R., Frank W., Fahr A., Kaiser W.A., Hilger I., Fluorescent Liposomes as Contrast Agents for In Vivo Optical Imaging of Edemas in Mice, Small, 4(2008)1240-6.

DY-676 for in vivo imaging

Lisy M.R., Goermar A., Thomas C., Pauli J., Resch-Genger U., Kaiser W.A., Hilger I., In Vivo Near-infrared Fluorescence Imaging of Carcinoembryonic Antigen-expressing Tumor Cells in Mice, Radiology, 247(2008)779-787.

DY-505, DY-555 and DY-635 in electrophoresis application

Volke D., Hoffmann R., Quantitative proteomics by fluorescent labeling of cysteine residues using a set of two cyanine-based or three rhodaminebased dyes, ELECTROPHORESIS, 29(2008)4516-4526.

DY-680 and DY-780 in proteomics

Riederer I.M., Herrero R.M., Leuba G., Riederer B.M., Serial protein labeling with infrared maleimide dyes to identify cysteine modifications, Journal of Proteomics, 71(2008)222-230.

DY-680 and DY-780 in proteomics (among others) / Review

Riederer B.M., Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis, Journal of Proteomics, 71(2008)231-244.

DY-547-Streptavidin

Mora J.R., Zielinsky T.L., Nelson B.P., Getts R.C., Protein detection enhanced by 3DNA dendrimer signal amplification, BioTechniques, 44(2008)815-818.

DY-665-X as standard for NIR-quantum yield measurements

Fischer G.M., Ehlers A.P., Zumbusch A., Daltrozzo E., Near-Infrared Dyes and Fluorophores Based on Diketopyrrolopyrroles, Angew. Chem. Intl. Ed., 46(2007)3750-3753.

DY-548 and DY-648 on microarrays:

Auer J., Bläss M., Schulze-Koops H., Russwurm S., Nagel T., Kalden J.R., Röllinghoff M., Beuscher H.U., Expression and regulation of CCL18 in synovial fluid neutrophils of patients with rheumatoid arthritis, Arthritis Research & Therapy, 9(2007)5R94, 12 pages.

DY-547 on microarrays

Kusnezow W., Banzon V., Schröder C., Schaal R., Hoheisel J.D., Rüffer S., Luft P., Duschl A., Syagailo Y.V., Antibody microarray-based profiling of complex specimens: systematic evaluation of labeling strategies, Proteomics, 7(2007)1786-1799.

DY-633-labeled secondary antibody

Derwinska K., Sauer U., Preininger C., Reproducibility of hydrogel slides in on-chip immunoassays with respect to scanning mode, spot circularity, and data filtering, Analytical Biochemistry, 370(2007)38-46.

DY-633-labeled secondary antibody

Derwinska K., Gheber L.A., Preininger C., A comparative analysis of polyurethane hydrogel for immobilization of IgG on chips, Analytica Chimica Acta, 592(2007)132-138.

DY-485XL in 4Pi microscopy:

Lang M.C., Engelhardt J., Hell S.W., 4Pi microscopy with linear fluorescence excitation, Optics Letters, 32(2007)259-61.

DY-485XL-labeled antibody in microscopy:

Staudt, T., Lang M., Medda R., Engelhardt J., Hell S. W., 2,2'-Thiodiethanol: a new water soluble mounting medium for high resolution optical microscopy, Microsc. Res. Tech., 70(2007) 1-9.

DY-633-biotin in microscopy:

Rinne J., Albarran B., Jylhävä J., Ihalainen T.O., Kankaanpää P., Hytönen V.P., Stayton P.S., Kulomaa M.S., Vihinen-Ranta M., Internalization of novel non-viral vector TAT-streptavidin into human cells, BMC Biotechnology, 7(2007)1-14.

DY-676 as contrast agent:

Lisy M.-R., Hartung A., Lang C., Schüler D., Richter W., Reichenbach J.R., Kaiser W.A., Hilger I., Fluorescent Bacterial Magnetic Nanoparticles as Bimodal Contrast Agents, Investigative Radiology, 42(2007)235-41.

DY-547-labeled cGMP:

Biskup C., Kusch J., Schulz E., Nache V., Schwede F., Lehmann F., Hagen V., Benndorf K., Relating lingand binding to activation gating in CNGA2 channels, nature, 446(2007)440-3.

DY-415, DY-550 and DY-631 for biochips:

Glasenapp C., Mönch W., Krause H., Zappe H., Biochip reader with dynamic holographic excitation and hyperspectral fluorescence detection, Journal of Biomedical Optics, 12(2007)014038, 8 pages.

Volkmer T., Becker C., Prodöhl A., Finger C., Schneider D., Assembly of a transmembrane b-Type cytochrome is mainly driven by transmembrane helix interactions, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1758(2006)1815-1822.

DY-676 in in-vivo imaging:

Lisy M.-R., Schüler E., Lehmann F., Czerney P., Kaiser W.A., Hilger I., Diagnosis of peritonitis using near-infrared optical imaging of in vivo labeled monocytes-macrophages, Journal of Biomedical Optics, 11(2006)064014, 9 pages.

DY-647-labeled streptavidin:

Kusnezow W., Syagailo Y.V., Rffer S., Baudenstiel N., Gauer C., Hoheisel J.D., Wild D., Goychuk I., Optimal Design of Microarray Immunoassays to Compensate for Kinetic Limitations, Molecular & Cellular Proteomics, 5.9(2006)1681-96.

DY-547 and DY-648-labeled benzylguanines:

Keppler A., Arrivoli C., Sironi L., Ellenberg J., Fluorophores for live cell imaging of AGT fusion proteins across the visible spectrum, BioTechniques, 41(2006)167-75.

DY-547 and DY-631 in confocal microscopy:

Michalakis S., Reisert J., Geiger H., Wetzel C., Zong X., Bradley J., Spehr M., Huellt S., Gerstner A., Pfeifer A., Hatt H., Yau K.-W., Biel M., Loss of CNGB1 Protein Leads to Olfactory Dysfunction and Subciliary Cyclic Nucleotide-gated Channel Trapping, J. Biol. Chem., 281(2006)35156-66.

DY-521XL in duplex-RT-PCR:

Dreier J., Stoermer M., Maede D., Burckhardt S., Kleesiek K., Enhanced Reverse Transcription-PCR Assay for Detection of Norovirus Genogroup I, Journal of Clinical Microbiology, 44(2006)2714-20.

DY-630 labeled peptide to study GPCRs:

Schneider E., Mayer M., Ziemek R., Li L., Hutzler C., Bernhardt G., Buschauer A., A Simple and Powerful Flow Cytometric Method for the Simultaneous Determination of Multiple Parameters at G Protein-Coupled Receptor Subtypes, ChemBioChem, 7(2006)1400-9.

DY-636 in a SNP hairpin probe:

Marmé N., Friedrich A., Denapaite D., Hakenbeck R., Knemeyer J.-P., Single nucleotide polymorphism analysis using different colored dye dimer probes, Chemical Physics Letters, 428(2006)440-5.

DY-520XL in cross correlation FCS:

Kosturko L.D., Maggipinto M.J., Korza G., Lee J.W., Carson J.H., Barbarese E., Heterogeneous Nuclear Ribonucleoprotein (hnRNP) E1 Binds to hnRNP A2 and Inhibits Translation of A2 Response Element mRNAs, Mol. Biol. Cell, 17(2006)3521-33.

DY-630-biotin in single molecule detection:

Jung S., Angerer B., Loescher F., Niehren S., Winkle J., Seeger S., Biotin-Functionalized Cellulose- Based Monolayers as Sensitive Interfaces for the Detection of Single Molecules, ChemBioChem, 7(2006)900-3.

DY-647 and DYQ-660 as FRET pair:

Käppel N.D.
, Dankbar D.M., Gauglitz G., DNA Quantification in Nanoliter Volumes, Microchim Acta , 154(2006)65-71.

DY-633-neutravidin as control on peptide microarrays:

Andresen H., Grötzinger C., Zarse K., Kreuzer O.J., Ehrentreich-Förster E., Bier F.F., Functional peptide microarrays for specific and sensitive antibody diagnostics, Proteomics, 6(2006)1376-84.

DY-633-streptavidin

Andresen H., Zarse K., Grötzinger C., Hollidt J.M., Ehrentreich-Förster E., Bier F.F., Kreuzer O.J., Development of peptide microarrays for epitope mapping of antibodies against the human TSH receptor, Journal of Immunological Methods, 315(2006)11-18.

DY-781 in sequencing application:

Rothenstein D., Haible D., Dasgupta I., Dutt N., Patil B.L., Jeske H.,Biodiversity and recombination of cassava-infecting begomoviruses from southern India, Archives of Virology, 151(2006)55-69.

DY-681-labeled primers in asymmetric PCR:

de Almeida R.A., Heuser T., Blaschke R., Bartram C.R., Janssen J.W.G., Control of MYEOV Protein Synthesis by Upstream Open Reading Frames, J. Biol. Chem, 281(2006) 695-704.

DY-633-labeled primers for microarray applications:

Sauer U., Preininger C., Hany-Schmatzberger R., Quick and simple: quality control of microarray data, Bioinformatics, 21(2005)1572-8.

DY-630 in DNA- and protein arrays:

Preininger C., Sauer U., Dayteg J., Pichler R., Optimizing processing parameters for signal enhancement of oligonucleotide and protein arrays on ARChip Epoxy, Bioelectrochemistry, 67(2005)155 - 162.

DY-633-labeled peptides:

von Nickisch-Rosenegk M., Ehrentreich-Forster E., Strehlo R., Christmann A., Bier F.F., Chemically synthesized zinc finger molecules as nano-addressable probes for double-stranded DNAs, Journal of Nanobiotechnology, 3(2005)5.

Detection of DY-681-labeled proteins:

Arndt V., Daniel C., Nastainczyk W., Alberti S., Höhfeld J., BAG-2 Acts as Inhibitor of the Chaperone-associated Ubiquitin Ligase CHIP, Molecular Biology of the Cell, 16(2005)5891-5900.

DY-547 and DY-631 in microscopy:

Michalakis S., Geiger H., Haverkamp S., Hofmann F., Gerstner A., Biel M., Impaired Opsin Targeting and Cone Photoreceptor Migration in the Retina of Mice Lacking the Cyclic Nucleotide-Gated Channel CNGA3, Investigative Ophthalmology & Visual Science, 46(2005)1516-1524.

DY-547 in microscopy:

Hüttl S., Michalakis S., Seeliger, Luo D.-G., Acar N., Geiger H., Hudl K., Mader R., Haverkamp S., Moser M., Pfeifer A., Gerstner A., Yau K.-W., Biel M., Impaired Channel Targeting and Retinal Degeneration in Mice Lacking the Cyclic Nucleotide-Gated Channel Subunit CNGB1, The Journal of Neuroscience, 25(2005)130-138

DY-681 and DY-781 in sequencing application:

Kaltenpoth M., Strohm E., Gadau J., Polymorphic microsatellite markers for a solitary digger wasp, the European beewolf (Philanthus triangulum; Hymenoptera, Sphecidae), Molecular Ecology Notes 4(2004)589-592.

Review

Peng X., Draney D., Near-IR fluorescent dyes for biological applications, LabPlus International, April/May 2004

EVOblue™30 in TIRF-microscopy:

Ruckstuhl T., Seeger S., Attoliter detection volumes by confocal total-internal-reflection fluorescence microscopy, Optics Letters, 29(2004)568-571.

Detection of DY-630-Maleimid-labeled proteins:

Diekmann S., Siegmund G., Roecker A., Klemm D.O., Regioselective nitrilotriacetic acid-cellulose-nickel-complexes for immobilisation of His6-tag proteins, Cellulose, 10(2003)53-63.

DY-630 on DNA-microarrays:

Preininger C., Sauer U., Quality control of chip manufacture and chip analysis using epoxy-chips as model, Sensors and Actuators B, 90(2003)98-103.

Optical properties of DY-630 and DY-635:

Czerney P., Lehmann F., Wenzel M., Buschmann V., Dietrich A., Mohr G.J., Taylor-Made Dyes for Fluorescence Correlation Spectroscopy (FCS), Biological Chemistry, 382(2001)495-49