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Malachite Green


CALI/FALI papers 1988-present

(Original research papers only)

1988-1991 (2)

1. Jay DG. Selective destruction of protein function by chromophore-assisted laser inactivation. Proc Natl Acad Sci U S A. 1988 Aug;85(15):5454-8.

2. Jay DG, Keshishian H. Laser inactivation of fasciclin I disrupts axon adhesion of grasshopper pioneer neurons. Nature. 1990 Dec 6;348(6301):548-50.

1992-1995 (7)

3. Indig G, Jay DG, Grabowski J. The photo-induced heat-release properties of Malachite green and Malachite green bound to protein. Biophys. J. 1992 61:631-638.

4.  Linden KG, Liao JC, Jay DG. Spatial specificity of chromophore assisted laser inactivation of protein function. Biophys J. 1992 Apr;61(4):956-62.

5. Diamond P, Mallavarapu A, Schnipper J, Booth J, Park L, O’Connor TP, Jay DG. Fasciclin I and II have distinct roles in the development of grasshopper pioneer neurons. Neuron. 1993 Sep;11(3):409-21

6. Liao, J.C, Roider, J. and Jay, D.G. (1994) Chromophore-Assisted Laser Inactivation of Proteins is Mediated by the Photogeneration of Free Radicals  Proc. Natl. Acad. Sci. USA 91:2659-2663.

7. Schmucker D, Su AL, Beermann A, Jackle H, Jay DG.  Chromophore-assisted laser inactivation of patched protein switches cell fate in the larval visual system of Drosophila. Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2664-8.

8. Chang HY, Takei K, Sydor AM, Born T, Rusnak F, Jay DG Asymmetric retraction of growth cone filopodia following focal inactivation of calcineurin. Nature. 1995 Aug 24;376(6542):686-90.

9. Liao JC, Berg LJ, Jay DG. Chromophore-assisted laser inactivation of subunits of the T-cell receptor in living cells is spatially restricted. Photochem Photobiol. 1995 Nov;62(5):923-9.

1996-1999 (12)

10. Wang FS, Wolenski JS, Cheney RE, Mooseker MS, Jay DG. Function of myosin-V in filopodial extension of neuronal growth cones. Science. 1996 Aug 2;273(5275):660-3.

11. Sydor AM, Su AL, Wang FS, Xu A, Jay DG. Talin and vinculin play distinct roles in filopodial motility in the neuronal growth cone.  J Cell Biol. 1996 Sep;134(5):1197-207.

12. Muller BK, Jay DG, Bonhoeffer F. Chromophore-assisted laser inactivation of a repulsive axonal guidance molecule. Curr Biol. 1996 Nov 1;6(11):1497-502.

13. Schroeder, R., Tautz, D. and Jay, D.G. Chromophore-Assisted Laser Inactivation of Even Skipped in Drosophila Phenocopies Genetic Loss of Function. Dev. Genes Evol.  1996 206:86-88

14. Lamb RF, Ozanne BW, Roy C, McGarry L, Stipp C, Mangeat P, Jay DG. Essential functions of ezrin in maintenance of cell shape and lamellipodial extension in normal and transformed fibroblasts.  Curr Biol. 1997 Sep 1;7(9):682-8.

15. Surrey T, Elowitz MB, Wolf PE, Yang F, Nedelec F, Shokat K, Leibler S. Chromophore-assisted light inactivation and self-organization of microtubules and motors. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4293-8. **

16. Takei K, Shin RM, Inoue T, Kato K, Mikoshiba K. Regulation of nerve growth mediated by inositol 1,4,5-trisphosphate receptors in growth cones. Science. 1998 Nov 27;282(5394):1705-8.

17. Schroder R, Jay DG, Tautz D. Elimination of EVE protein by CALI in the short germ band insect Tribolium suggests a conserved pair-rule function for even skipped. Mech Dev. 1999 Feb;80(2):191-5.

18. Castelo L, Jay DG. Radixin is involved in lamellipodial stability during nerve growth cone motility. Mol Biol Cell. 1999 May;10(5):1511-20.

19. Takei K, Chan TA, Wang FS, Deng H, Rutishauser U, Jay DG. The neural cell adhesion molecules L1 and NCAM-180 act in different steps of neurite outgrowth.  J Neurosci. 1999 Nov 1;19(21):9469-79

20. Liu CW, Lee G, Jay DG. Tau is required for neurite outgrowth and growth cone motility of chick sensory neurons. Cell Motil Cytoskeleton. 1999;43(3):232-42.

21. Grate D, Wilson C. Laser-mediated, site-specific inactivation of RNA transcripts. Proc Natl Acad Sci U S A. 1999 May 25;96(11):6131-6. **

2000-2003 (18)

22. Baugh C, Grate D, Wilson C. 2.8 A crystal structure of the malachite green aptamer. J Mol Biol. 2000 Aug 4;301(1):117-28 **.

23. Mack TG, Koester MP, Pollerberg GE. The microtubule-associated protein MAP1B is involved in local stabilization of turning growth cones. Mol Cell Neurosci. 2000 Jan;15(1):51-65. **

24. Graner E, Mercadante AF, Zanata SM, Martins VR, Jay DG, Brentani RR. Laminin-induced PC-12 cell differentiation is inhibited following laser inactivation of cellular prion protein. FEBS Lett. 2000 Oct 6;482(3):257-60.

25. Lamb RF, Roy C, Diefenbach TJ, Vinters HV, Johnson MW, Jay DG, Hall A. The TSC1 tumour suppressor hamartin regulates cell adhesion through ERM proteins and the GTPase Rho. Nat Cell Biol. 2000 May;2(5):281-7.

26. Inoue T, Kikuchi K, Hirose K, Iino M, Nagano T. Small molecule-based laser inactivation of inositol 1,4,5-trisphosphate receptor. Chem Biol. 2001 Jan;8(1):9-15. **

27. Rajfur Z, Roy P, Otey C, Romer L, Jacobson K. Dissecting the link between stress fibres and focal adhesions by CALI with EGFP fusion proteins. Nat Cell Biol. 2002 Apr;4(4):286-93. **

28. Rubenwolf S, Niewohner J, Meyer E, Petit-Frere C, Rudert F, Hoffmann PR, Ilag LL. Functional proteomics using chromophore-assisted laser inactivation. Proteomics. 2002 Mar;2(3):241-6. **

29. Beck S, Sakurai T, Eustace BK, Beste G, Schier R, Rudert F, Jay DG.  Fluorophore-assisted light inactivation: a high-throughput tool for direct target validation of proteins. Proteomics. 2002 Mar;2(3):247-55.

30. Sakurai T, Wong E, Drescher U, Tanaka H, Jay DG. Ephrin-A5 restricts topographically specific arborization in the chick retinotectal projection in vivo. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10795-800.

31. Diefenbach TJ, Latham VM, Yimlamai D, Liu CA, Herman IM, Jay DG. Myosin 1c and myosin IIB serve opposing roles in lamellipodial dynamics of the neuronal growth cone. J Cell Biol. 2002 Sep 30;158(7):1207-17.

32. Hoffman-Kim D, Kerner JA, Chen A, Xu A, Wang TF, Jay DG. pp60(c-src) is a negative regulator of laminin-1-mediated neurite outgrowth in chick sensory neurons. Mol Cell Neurosci. 2002 Sep;21(1):81-93.

33. Marek KW, Davis GW.  Transgenically encoded protein photoinactivation (FlAsH-FALI): acute inactivation of synaptotagmin I. Neuron. 2002 Dec 5;36(5):805-13. **

34. Nakai Y, Kamiguchi H. Migration of nerve growth cones requires detergent-resistant membranes in a spatially defined and substrate-dependent manner. J Cell Biol. 2002 Dec 23;159(6):1097-108. **

35. Wong EV, David S, Jacob MH, Jay DG. Inactivation of myelin-associated glycoprotein enhances optic nerve regeneration. J Neurosci. 2003 Apr 15;23(8):3112-7.

36. Pitsillides CM, Joe EK, Wei X, Anderson RR, Lin CP. Selective cell targeting with light-absorbing microparticles and nanoparticles.  Biophys J. 2003 Jun;84(6):4023-32. **

37. Wang FS, Liu CW, Diefenbach TJ, Jay DG. Modeling the role of myosin 1c in neuronal growth cone turning. Biophys J. 2003 Nov;85(5):3319-28.

38. Tour O, Meijer RM, Zacharias DA, Adams SR, Tsien RY. Genetically targeted chromophore-assisted light inactivation. Nat Biotechnol. 2003 Dec;21(12):1505-8. **

39. Poskanzer KE, Marek KW, Sweeney ST, Davis GW. Synaptotagmin I is necessary for compensatory synaptic vesicle endocytosis in vivo. Nature. 2003 426:559-63. **

2004-2007 (15)

40. Eustace BK, Sakurai T, Stewart JK, Yimlamai D, Unger C, Zehetmeier C, Lain B, Torella C, Henning SW, Beste G, Scroggins BT, Neckers L, Ilag LL, Jay DG. Functional proteomic screens reveal an essential extracellular role for hsp90 alpha in cancer cell invasiveness. Nat Cell Biol. 2004.

41. Yogo T, Kikuchi K, Inoue T, Hirose K, Iino M, Nagano T. Modification of intracellular Ca2+ dynamics by laser inactivation of inositol 1,4,5-trisphosphate receptor using membrane-permeant probes. Chem Biol. 2004 Aug;11(8):1053-8. **

42. Marks KM, Braun PD, Nolan GP. A general approach for chemical labeling and rapid, spatially controlled protein inactivation. Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):9982-7.  **

43. Sloan KE, Eustace BK, Stewart JK, Zehetmeier C, Torella C, Simeone M, Roy JE, Unger C, Louis DN, Ilag LL, Jay DG.  CD155/PVR plays a key role in cell motility during tumor cell invasion and migration.  BMC Cancer. 2004 Oct 7;41:73.

44. Horstkotte E, Schroder T, Niewohner J, Thiel E, Jay DG, Henning SW. Toward understanding the mechanism of chromophore-assisted laser inactivation–evidence for the primary photochemical steps. Photochem Photobiol. 2005 Mar-Apr;81(2):358-66.

45. Hauptschein RS, Sloan KE, Torella C, Moezzifard R, Giel-Moloney M, Zehetmeier C, Unger C, Ilag LL, Jay DG. Functional proteomic screen identifies a modulating role for CD44 in death receptor-mediated apoptosis. Cancer Res. 2005 Mar 1;65(5):1887-96.

46. Tanabe T, Oyamada M, Fujita K, Dai P, Tanaka H, Takamatsu T.  Multiphoton excitation-evoked chromophore-assisted laser inactivation using green fluorescent protein. Nat Methods. 2005 Jul;2(7):503-5 **

47. de Anda FC, Pollarolo G, Da Silva JS, Camoletto PG, Feiguin F, Dotti CG. Centrosome localization determines neuronal polarity.Nature. 2005 Aug 4;436(7051):704-8.

48. Sloan KE, Stewart JK, Treloar AF, Matthews RT, Jay DG. CD155/PVR enhances glioma cell dispersal by regulating adhesion signaling and focal adhesion dynamics. Cancer Res. 2005 Dec 1;65(23):10930-7.

49. Bulina ME, Chudakov DM, Britanova OV, Yanushevich YG, Staroverov DB, Chepurnykh TV, Merzlyak EM, Shkrob MA, Lukyanov S, Lukyanov KA.  A genetically encoded photosensitizer. Nat Biotechnol. 2006 Jan;24(1):95-9.  **

50. Yan P, Xiong Y, Chen B, Negash S, Squier TC, Mayer MU. Fluorophore-assisted light inactivation of calmodulin involves singlet-oxygen mediated cross-linking and methionine oxidation. Biochemistry. 2006 Apr 18;45(15):4736-48. **

51. Guo J, Chen H, Puhl 3rd HL, Ikeda SR. Fluorophore-assisted light inactivation produces both targeted and collateral effects on N-type calcium channel modulation in rat sympathetic neurons. J. Gen Physiol. 2006 Jul 27; [Epub ahead of print]

52. Vitriol EA, Uetrecht AC, Shen F, Jacobson K, Bear JE. Enhanced EGFP-chromophore-assisted laser inactivation using deficient cells rescued with functional EGFP-fusion proteins. Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6702-7. Epub 2007 Apr 9.

53.  Rahmanzadeh R, Huttmann G, Gerdes J, Scholzen T. Chromophore-assisted light inactivation of pKi-67 leads to inhibition of ribosomal RNA synthesis. Cell Prolif. 2007 Jun;40(3):422-30.

54.  Koester MP, Muller O, Pollerberg GE Adenomatous polyposis coli is differentially distributed in growth cones and modulates their steering JOURNAL OF NEUROSCIENCE   Volume: 27   Issue: 46   Pages: 12590-12600   Published: NOV 14 2007

2008-2011 (26)

55. Lee J, Yu P, Xiao X, Kodadek T. A general system for evaluating the efficiency of chromophore-assisted light inactivation (CALI) of proteins reveals Ru(ii) tris-bipyridyl as an unusually efficient “warhead”. Mol Biosyst. 2008 Jan;4(1):59-65. Epub 2007 Oct

56. Bruneau EG, Brenner DS, Kuwada JY, Akaaboune M. Acetylcholine receptor clustering is required for the accumulation and maintenance of scaffolding proteins.  Curr Biol. 2008 Jan 22;18(2):109-15.

57. Heerssen H, Fetter RD, Davis GW. Clathrin dependence of synaptic-vesicle formation at the Drosophila neuromuscular junction. Curr Biol. 2008 Mar 25;18(6):401-9.

58. AbeTK, HondaT, Takei K, MikoshibaK, Hoffman-KimD, JayDG, and KuwanoR (2008) Dynactin is Essential for Growth Cone AdvanceBiochem Biophys Res Comm 372:418-422.

59. Yogo, T., Y. Urano, et al. (2008). “Selective photoinactivation of protein function through environment-sensitive switching of singlet oxygen generation by photosensitizer.” Proc Natl Acad Sci U S A 105(1): 28-32.

60. McLean MA, Rajfur Z, Chen Z, Humphrey D, Yang B, Sligar SG, Jacobson K. Mechanism of Chromophore Assisted Laser Inactivation Employing Fluorescent Proteins. Anal Chem. 2009 Jan 29. [Epub ahead of print]

61. Keppler A, Ellenberg J Chromophore-Assisted Laser Inactivation of alpha- and gamma-Tubulin SNAP-tag Fusion Proteins inside Living Cells  ACS CHEMICAL BIOLOGY   Volume: 4   Issue: 2   Pages: 127-138   Published: FEB 2009

62. Iketani M, Imaizumi C, Nakamura F, Jeromin A, Mikoshiba K, Goshima Y, Takei K. Regulation of neurite outgrowth mediated by neuronal calcium sensor-1 and inositol 1,4,5-trisphosphate receptor in nerve growth cones. 2009 Neuroscience.  Jul 7;161(3):743-52.

63. Carpentier P, Violot S, Blanchoin L, Bourgeois D. Structural basis for the phototoxicity of the fluorescent protein KillerRed. FEBS Lett. 2009 Sep 3;583(17):2839-42

64. Bagci T, Wu JK, Pfannl R, Ilag LL, Jay DG. (2009) Autrocrine Semaphorin 3A signaling promotes glioblastoma dispersal. Oncogene 8;28(40):3537-50.  PMC journal in progress.

65. Cai Y, Rossier O, Gauthier NC, Biais N, Fardin MA, Zhang X, Miller LW, Ladoux B, Cornish VW, Sheetz MP. Cytoskeletal coherence requires myosin-IIA contractility. J Cell Sci. 2010 Feb 1;123(Pt 3):413-23. Epub 2010 Jan 12.

66. Monier B, Pélissier-Monier A, Brand AH, Sanson B. An actomyosin-based barrier inhibits cell mixing at compartmental boundaries in Drosophila embryos. Nat Cell Biol. 2010 Jan;12(1):60-5; sup pp 1-9.

67. Lee J, Udugamasooriya DG, Lim HS, Kodadek T. Potent and selective photo-inactivation of proteins with peptoid-ruthenium conjugates. Nat Chem Biol. 2010 Apr;6(4):258-260. Epub 2010 Mar 14.

68. Ojida A, Fujishima SH, Honda K, Nonaka H, Uchinomiya SH, Hamachi I. (2010) Binuclear Ni(II)-DpaTyr complex as a high affinity probe for an oligo-aspartate Tag tethered to proteins. Chem Asian J. 2010 Apr 1;5(4):877-86.

69. Kapustina M, Vitriol E, Elston TC, Loew LM, Jacobson K. (2010) Modeling capping protein FRAP and CALI experiments reveals in vivo regulation of actin dynamics. Cytoskeleton (Hoboken).  Aug;67(8):519-34.

70. Roy A, Carpentier P, Bourgeois D, Field M. Diffusion pathways of oxygen species in the phototoxic fluorescent protein KillerRed. Photochem Photobiol Sci. 2010 Aug 31. [Epub ahead of print]

71. Ou G, Stuurman N, D’Ambrosio M, Vale RD. Polarized myosin produces unequal-size daughters during asymmetric cell division. Science. 2010 Oct 29;330(6004):677-80. Epub 2010 Sep 30.

72. Duan XR, Liu LB, Feng XL, et al. Assemblies of Conjugated Polyelectrolytes with Proteins for Controlled Protein Photoinactivation ADVANCED MATERIALS   Volume: 22   Issue: 14   Pages: 1602-+   Published: APR 12 2010

73. Takemoto K, Matsuda T, McDougall M, Klaubert DH, Hasegawa A, Los GV, Wood KV, Miyawaki A, Nagai T. Chromophore-Assisted Light Inactivation of HaloTag Fusion Proteins Labeled with Eosin in Living Cells. ACS Chem Biol. 2011 May 20;6(5):401-6.

74. Ragàs X, Cooper LP, White JH, Nonell S, Flors C. Quantification of photosensitized singlet oxygen production by a fluorescent protein. Chemphyschem. 2011 Jan 17;12(1):161-5. doi: 10.1002/cphc.201000919. Epub 2010 Dec 5

75. Morton RA, Luo G, Davis MI, Hales TG, Lovinger DM. Fluorophore assisted light inactivation (FALI) of recombinant 5-HT(3)A receptor constitutive internalization and function. Mol Cell Neurosci. 2011 Feb 19

76. Habets RL, Verstreken P. FlAsH-FALI inactivation of a protein at the third-instar neuromuscular junction. Cold Spring Harb Protoc. 2011 Apr 1;2011:pdb.prot5597. doi: 10.1101/pdb.prot5597.

77. Sato Y, Iketani M, Kurihara Y, Yamaguchi M, Yamashita N, Nakamura F, Arie Y, Kawasaki T, Hirata T, Abe T, Kiyonari H, Strittmatter SM, Goshima Y, Takei K. Cartilage acidic protein-1B (LOTUS), an endogenous Nogo receptor antagonist for axon tract formation. Science. 2011 Aug 5;333(6043):769-73.

78. Snellman Josefin; Mehta Bhupesh; Babai Norbert; et al.Acute destruction of the synaptic ribbon reveals a role for the ribbon in vesicle priming NATURE NEUROSCIENCE  Volume: 14   Issue: 9   Pages: 1135-U262   DOI: 10.1038/nn.2870   Published: SEP 2011

79. Li Xiang; Kapoor Tarun M. An Optical Switch for a Motor Protein CHEMBIOCHEM  Volume: 12   Issue: 15   Pages: 2265-2266   DOI: 10.1002/cbic.201100439   Published: OCT 17 2011

80. Serebrovskaya, E.O., Gorodnicheva, T.V., Ermakova, G.V., Solovieva, E.A., Sharonov, G.V., Zagaynova, E.V., Chudakov, D.M., Lukyanov, S., Zaraisky, A.G. & Lukyanov, K.A. 2011, “Light-induced blockage of cell division with a chromatin-targeted phototoxic fluorescent protein”, Biochemical Journal, vol. 435, no. 1, pp. 65-71.

2012-2015 (6 and counting)

81. Baumgart Florian; Rossi Andrea; Verkman A. S. Light inactivation of water transport and protein-protein interactions of aquaporin-Killer Red chimeras  JOURNAL OF GENERAL PHYSIOLOGY  Volume: 139   Issue: 1   Pages: 83-91   DOI: 10.1085/jgp.201110712   Published: JAN 2012

82. Jarvela T, Linstedt AD. Irradiation-induced protein inactivation reveals Golgi enzyme cycling to cell periphery. J. Cell Sci., 2012. 125:973-980

83. Higurashi M, Iketani M, Takei K, Yamashita N, Aoki R, Kawahara N, Goshima Y. Localized role of CRMP1 and CRMP2 in neurite outgrowth and growth cone steering. Dev Neurobiol. 2012 Feb 29. doi: 10.1002/dneu.22017. [Epub ahead of print]

84. Nadar VC, Lin S, Baas PW. Microtubule redistribution in growth cones elicited by focal inactivation of kinesin-5. J Neurosci 2012, 32: 5783–5794.

85. Kobrinsky E, Lee JH, Soldatov NM.Selective fluorophore-assisted light inactivation of voltage-gated calcium channels. Channels (Austin). 2012 May-Jun;6(3):154-6

86. Iketani M, Iizuka A, Sengoku K, Kurihara Y, Nakamura F, Sasaki Y, Sato Y, Yamane M, Matsushita M, Nairn AC, Takamatsu K, Goshima Y, Takei K.  Regulation of neurite outgrowth mediated by localized phosphorylation of protein translational factor eEF2 in growth cones.  Dev Neurobiol. 2012 Sep 24. doi: 10.1002/dneu.22058. [Epub ahead of print]