MBIC / FBNP Publications

Publications related to Fluorescent Probes for Networks and Pathways technologies

• Zanotti KJ, Silva GL, Creeger Y, Robertson KL, Waggoner AS, Berget PB, Armitage BA. (2011) Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments. Org Biomol Chem. 9(4):1012-20.  Epub 2010 Dec 22.  PMID: 21180706

• Fisher GW, Adler SA, Fuhrman MH, Waggoner AS, Bruchez MP, Jarvik JW.  (2010) Detection and quantification of beta2AR internalization in living cells using FAP-based biosensor technology. J Biomol Screen. 15(6):703-9.  Epub 2010 May 20.  PMID: 20488980

• Holleran J, Brown D, Fuhrman MH, Adler SA, Fisher GW, Jarvik JW. (2010) Fluorogen-activating proteins as biosensors of cell-surface proteins in living cells. Cytometry A. 77(8):776-82.  PMID: 20653017

• Szent-Gyorgyi C, Schmidt BF, Fitzpatrick JA, Bruchez MP.  (2010) Fluorogenic dendrons with multiple donor chromophores as bright genetically targeted and activated probes. J Am Chem Soc. 132(32):11103-9.  PMID: 20698676

• Falco CN, Dykstra KM, Yates BP, Berget PB. (2009) scFv-based fluorogen activating proteins and variable domain inhibitors as fluorescent biosensor platforms. Biotechnol J. 4(9):1328-36. PMID: 19606431

• Fitzpatrick JA, Yan Q, Sieber JJ, Dyba M, Schwarz U, Szent-Gyorgyi C, Woolford CA, Berget PB, Waggoner AS, Bruchez MP. (2009) STED nanoscopy in living cells using Fluorogen Activating Proteins. Bioconjug Chem. 20(10):1843-1847.  PMID: 20976031

• Lusvarghi S, Kim JM, Creeger Y, Armitage BA. (2009) Refined multivalent display of bacterial spore-binding peptides. Org Biomol Chem. 7(9):1815-20.  Epub 2009 Mar 10.  PMID: 19590776

• Shank NI, Zanotti KJ, Lanni F, Berget PB, Armitage BA. (2009) Enhanced photostability of genetically encodable fluoromodules based on fluorogenic cyanine dyes and a promiscuous protein partner. J Am Chem Soc. 131(36):12960-9.  PMID: 19737016

• Armitage BA, Berget PB. (2008) Chemistry. An enlightening structure-function relationship. Science. 319(5867):1195-6.  PMID: 18309067

• Constantin TP, Silva GL, Robertson KL, Hamilton TP, Fague K, Waggoner AS, Armitage BA. (2008) Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. Org Lett. 10(8):1561-4.  Epub 2008 Mar 14.  PMID: 18338898

• Ediz V, Lee JL, Armitage BA, Yaron D. (2008) Molecular engineering of torsional potentials in fluorogenic dyes via electronic substituent effects. J Phys Chem A. 112(40):9692-701.  Epub 2008 Sep 11.  PMID: 18785691

• Ozhalici-Unal H, Pow CL, Marks SA, Jesper LD, Silva GL, Shank NI, Jones EW, Burnette JM 3rd, Berget PB, Armitage BA. (2008) A rainbow of fluoromodules: a promiscuous scFv protein binds to and activates a diverse set of fluorogenic cyanine dyes. J Am Chem Soc. 130(38):12620-1. Epub 2008 Aug 30.  PMID: 18761447

• Szent-Gyorgyi C, Schmidt BF, Creeger Y, Fisher GW, Zakel KL, Adler S, Fitzpatrick JA, Woolford CA, Yan Q, Vasilev KV, Berget PB, Bruchez MP, Jarvik JW, Waggoner A.  (2008) Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nat Biotechnol. 26(2):235-40.  Epub 2007 Dec 23. Erratum in: Nat Biotechnol. 2008 Apr;26(4):470. Schmidt, Brigitte A [corrected to Schmidt, Brigitte F]. PMID: 18157118

Additional MBIC Publications

• Corti, P., Young, S., Chen, C.-Y., Patrick, M.J., Rochon, E., Pekkan, K., and Roman, B. (2011) Interaction between alk1 and blood flow in development of arteriovenous malformations. Development. 138(8):1573-82

• Mittal R, Bruchez MP. (2011) Biotin-4-fluorescein based fluorescence quenching assay for determination of biotin binding capacity of streptavidin conjugated quantum dots. Bioconjug Chem. 22(3):362-8. Epub 2011 Feb 11.  PMID: 21314110

• Patrick, M.J., Chen, C.-Y., Frakes, D.H., Dur, O., Pekkan, K. (2011) Cellular-level near-wall unsteadiness of high-hematocrit erythrocyte flow using confocal microPIV. Exp Fluids 50:887–904

• Roy S, Zanotti KJ, Murphy CT, Tanious FA, Wilson WD, Ly DH, Armitage BA. (2011) Kinetic discrimination in recognition of DNA quadruplex targets by guanine-rich heteroquadruplex-forming PNA probes. Chem Commun (Camb). 47(30):8524-6.  Epub 2011 Jun 30.  PMID: 21717030

• Sahu B, Sacui I, Rapireddy S, Zanotti KJ, Bahal R, Armitage BA, Ly DH. (2011) Synthesis and characterization of conformationally preorganized, (R)-diethylene glycol-containing γ-peptide nucleic acids with superior hybridization properties and water solubility. J Org Chem. 76(14):5614-27.  Epub 2011 Jun 15.  PMID: 21619025

• Stadler AL, Delos Santos JO, Stensrud ES, Dembska A, Silva GL, Liu S, Shank NI, Kunttas-Tatli E, Sobers CJ, Gramlich PM, Carell T, Peteanu LA, McCartney BM, Armitage BA. (2011) Fluorescent DNA nanotags featuring covalently attached intercalating dyes: synthesis, antibody conjugation, and intracellular imaging. Bioconjug Chem. 22(8):1491-502.  Epub 2011 Jul 22.  PMID: 21755981

• Stadler AL, Renikuntla BR, Yaron D, Fang AS, Armitage BA. (2011) Substituent effects on the assembly of helical cyanine dye aggregates in the minor groove of a DNA template. Langmuir. 27(4):1472-9.  Epub 2010 Dec 21.  PMID: 21174432

• Damerla RR, Knickelbein KE, Kepchia D, Jackson A, Armitage BA, Eckert KA, Opresko PL. (2010) Telomeric repeat mutagenicity in human somatic cells is modulated by repeat orientation and G-quadruplex stability. DNA Repair (Amst). 9(11):1119-29.  Epub 2010 Aug 25.  PMID: 20800555

• Sengar RS, Nigam A, Ernst LA, Waggoner AS, Gratton E, Holub O, and Wiener EC (2010) Electronic substituent effects via remote substitution on the chromophores of heptacyanine dyes, Contrast Media & Molecular Imaging 4(6):264–265.

• Ballou B, Ernst LA, Andreko S, Fitzpatrick JA, Lagerholm BC, Waggoner AS, Bruchez MP.  (2009) Imaging vasculature and lymphatic flow in mice using quantum dots. Methods Mol Biol. 574:63-74. PMID: 19685300

• Buck TE, Rao A, Coelho LP, Fuhrman MH, Jarvik JW, Berget PB, Murphy RF. (2009) Cell cycle dependence of protein subcellular location inferred from static, asynchronous images. Conf Proc IEEE Eng Med Biol Soc. 2009:1016-9.  PMID: 19963740

• Fitzpatrick JA, Andreko SK, Ernst LA, Waggoner AS, Ballou B, Bruchez MP. (2009) Long-term persistence and spectral blue shifting of quantum dots in vivo. Nano Lett. 9(7):2736-41.  PMID: 19518087

• Lusvarghi S, Murphy CT, Roy S, Tanious FA, Sacui I, Wilson WD, Ly DH, Armitage BA. (2009) Loop and backbone modifications of peptide nucleic acid improve g-quadruplex binding selectivity. J Am Chem Soc. 131(51):18415-24.  PMID: 19947597

• Mittal R, Bruchez MP. (2009) Calibration of Flow Cytometry for Quantitative Quantum Dot Measurements. Curr Protoc Cytom. Chapter 6:Unit6.26.  PMID: 20953266

• Ozhalici-Unal H, Armitage BA. (2009) Fluorescent DNA nanotags based on a self-assembled DNA tetrahedron. ACS Nano. 3(2):425-33.  PMID: 19236081

• Shank NI, Zanotti KJ, Lanni F, Berget PB, Armitage BA. (2009) Enhanced photostability of genetically encodable fluoromodules based on fluorogenic cyanine dyes and a promiscuous protein partner. J Am Chem Soc. 131(36):12960-9.  PMID: 19737016

• Waggoner AS, Ernst LA, Ballou B (2009) Building new fluorescent probes, in Biomedical Optical Imaging, ed. Farkas D and Fujimoto JG.

• Wang Y., Dur O., Patrick M.J., Tinney J.P., Tobita K., Keller B.B., Pekkan K. (2009) Aortic Arch Morphogenesis and Flow Modeling in the Chick Embryo. Ann Biomed Eng. 37(6):1069-81

• Ballou B, Ernst LA, Andreko S, Bruchez MP, Lagerholm BC, Waggoner AS (2008) Long-Term Retention of Fluorescent Quantum Dots In Vivo, in Nanomaterials for Application in Medicine and Biology, ed. Giersig M and Khomutov GB.

• Daneshvar H, Nelms J, Muhammad O, Jackson H, Tkach J, Davros W, Peterson T, Vogelbaum MA, Bruchez MP, Toms SA.  (2008) Imaging characteristics of zinc sulfide shell, cadmium telluride core quantum dots. Nanomedicine (Lond). 3(1):21-9.  PMID: 18393664

• Phillippi JA, Miller E, Weiss L, Huard J, Waggoner A, Campbell P (2008) Microenvironments engineered by inkjet bioprinting spatially direct adult stem cells toward muscle- and bone-like subpopulations, Stem Cells 26(1):127-34.

• Weinstein S, Pane D, Ernst LA, Warren-Rhodes K, Dohm JM, Hock AN, Piatek JL, Emani S, Lanni F, Wagner M, Fisher GW, Minkley E, Dansey LE, Smith T, Grin EA, Stubbs K, Thomas G, Cockell CS, Marinangeli L, Ori GG, Heys S, Teza JP, Moersch JE, CoppinP, Diaz GC, Wettergreen DS, Cabrol NA, and Waggoner AS (2008) Application of pulsed-excitation fluorescence imager for daylight detection of sparse life in tests in the Atacama Desert, J. Geophys. Res. 113, G01S90, doi:10.1029/2006JG000319

• Armitage BA. (2007) The rule of four. Nat Chem Biol. 3(4):203-4.   PMID: 17372603

• Ballou B, Ernst LA, Andreko S, Harper T, Fitzpatrick JA, Waggoner AS, Bruchez MP. (2007) Sentinel lymph node imaging using quantum dots in mouse tumor models. Bioconjug Chem. 18(2):389-96.  Epub 2007 Jan 31.  PMID: 17263568

• Benvin AL, Creeger Y, Fisher GW, Ballou B, Waggoner AS, Armitage BA. (2007) Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates. J Am Chem Soc. 129(7):2025-34.  Epub 2007 Jan 26.  PMID: 17256855

• Chakraborty SK, Fitzpatrick JA, Phillippi JA, Andreko S, Waggoner AS, Bruchez MP, Ballou B. (2007) Cholera toxin B conjugated quantum dots for live cell labeling. Nano Lett. 7(9):2618-26.  Epub 2007 Jul 31.  PMID: 17663586

• Patrick, M. J., Ernst, L. A., Waggoner, A. S., Thai, D., Tai, D., and Salama, G. (2007) Enhanced Aqueous Solubility of Long Wavelength Voltage-Sensitive Dyes by Covalent Attachment of Polyethylene Glycol Org. Biomol. Chem., 5, 3347-3353

• Rapireddy S, He G, Roy S, Armitage BA, Ly DH. (2007) Strand invasion of mixed-sequence B-DNA by acridine-linked, gamma-peptide nucleic acid (gamma-PNA). J Am Chem Soc. 129(50):15596-600.  pub 2007 Nov 21.  PMID: 18027941

• Roy S, Tanious FA, Wilson WD, Ly DH, Armitage BA. (2007) High-affinity homologous peptide nucleic acid probes for targeting a quadruplex-forming sequence from a MYC promoter element. Biochemistry. 46(37):10433-43.  Epub 2007 Aug 24.  PMID: 17718513

• Silva GL, Ediz V, Yaron D, Armitage BA. (2007) Experimental and computational investigation of unsymmetrical cyanine dyes: understanding torsionally responsive fluorogenic dyes. J Am Chem Soc. 129(17):5710-8.  Epub 2007 Apr 6.  PMID: 17411048

• Robertson KL, Yu L, Armitage BA, Lopez AJ, Peteanu LA. (2006) Fluorescent PNA probes as hybridization labels for biological RNA. Biochemistry. 45(19):6066-74.  PMID: 16681379