Biological Photonic Crystals: Diatoms Dye functionalization of biological silica nanostructures Dissertation for Obtaining the Degree Doctor of Natural Sciences - Dr. rer. nat. - Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) Submitted by Melanie Kucki to the University of Kassel, Department of Natural Sciences Biological Photonic Crystals: Diatoms Dye functionalization of biological silica nanostructures Dissertation for Obtaining the Degree Doctor of Natural Sciences - Dr. rer. nat. - Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) Presented at University of Kassel, Department of Natural Sciences by Melanie Kucki Kassel, April 2009 „I certify that I made this thesis independently, without any disallowed assistance and without use of others than the aid indicated in this thesis. Content which is literally or in general manner taken out of published or unpublished sources is marked. This is also valid for photographs, drawings, sketches and other image presentation. No part of this thesis has been previously submitted and approved for the award of a degree by this or any other university.” „Hiermit versichere ich, dass ich die vorliegende Dissertation selbständig und ohne unerlaubte Hilfe angefertigt und keine anderen als die in der Dissertation angegebenen Hilfsmittel benutzt habe. Alle Stellen, die wörtlich oder sinngemäß aus veröffentlichten oder unveröffentlichten Schriften entnommen sind, habe ich als solche kenntlich gemacht. Dies gilt auch für Fotos, Zeichnungen, Skizzen und andere bildliche Darstellungen. Kein Teil dieser Arbeit ist in einem anderen Promotions- oder Habilitationsverfahren verwendet worden.“ Kassel, 06.04.2009 Accepted as dissertation by the Department of Natural Sciences, University of Kassel, Germany Advisor: private lecturer Dr. Thomas Fuhrmann-Lieker First Referee: private lecturer Dr. Thomas Fuhrmann-Lieker Second Referee: Prof. em. Dr. Hartmut Follmann Date of defence: 26.05.2009 Committee: private lecturer Dr. Thomas Fuhrmann-Lieker Prof. em. Dr. Hartmut Follmann Prof. Dr. Joseph Salbeck Prof. Dr. Markus Maniak The experimental part of this work was performed from August 2003 to September 2006. Parts of this work are published in: Fuhrmann T., Landwehr S.,El Rharbi-Kucki M., Sumper M. (2004); Diatoms as living photonic crystals; Applied Physics B Vol. 78, Nr. 3-4: 257-260 Kucki M., Landwehr S., Rühling H., Maniak M., Fuhrmann-Lieker T. (2006); Light-emitting biological photonic crystals – the bioengineering of metamaterials, Proceedings of SPIE Vol. 6182, Photonic Crystal, Material and Devices III, pp. 61821S-1 - 61821S-9 TABLE OF CONTENTS (INHALTSVERZEICHNIS) Table of Contents (Inhaltsverzeichnis).......................................................................I 1 Motivation ..................................................................................................................... 1 2 Background................................................................................................................... 5 2.1 Photonic Crystals ............................................................................................................ 5 2.1.1 1D-Photonic Crystals................................................................................................................. 7 2.1.2 2D-Photonic Crystals................................................................................................................. 8 2.1.3 3D-Photonic Crystals................................................................................................................. 8 2.1.4 Photonic crystal waveguides...................................................................................................... 9 2.1.5 Influence of the photonic structure on an integrated emitter ................................................... 10 2.2 Photonic Devices in Nature .......................................................................................... 12 2.2.1 1D-Photonic crystals (multilayer systems) .............................................................................. 15 2.2.2 2D-Photonic crystals................................................................................................................ 15 2.2.3 3D-Photonic crystals................................................................................................................ 17 2.2.4 Combination of fluorescent pigments and photonic crystal structure:..................................... 17 2.3 Biomineralization.......................................................................................................... 18 2.3.1 Biosilification .......................................................................................................................... 21 2.3.2 Silica forming sponges ............................................................................................................ 23 2.3.3 Testate amoebae ...................................................................................................................... 24 2.4 Diatoms .......................................................................................................................... 27 2.4.1 Structure of the diatom cell with focus on Coscinodiscus granii and Coscinodiscus wailesii 28 2.4.2 Vegetative cell cycle and cell wall formation.......................................................................... 35 2.4.3 Character and chemistry of the diatom cell wall ..................................................................... 39 2.4.4 Diatom Silica (Bio)technology................................................................................................ 42 2.4.5 Adaptation to light................................................................................................................... 43 2.5 Fluorescence and Laser Dyes....................................................................................... 47 2.5.1 Rhodamines ............................................................................................................................. 48 2.5.2 LysoSensor™ Yellow/Blue DND-160 .................................................................................... 52 2.5.3 Oxazone................................................................................................................................... 53 2.5.4 Stilbene.................................................................................................................................... 54 3 Experimental............................................................................................................... 56 3.1 Organisms...................................................................................................................... 56 3.2 Cultivation..................................................................................................................... 56 3.2.1 Seawater Medium for marine Diatoms.................................................................................... 56 3.2.2 Culture conditions.................................................................................................................... 57 3.3 In vivo-Fluorochromation of diatom cells .................................................................. 59 3.3.1 Commercially available fluorescent dyes ................................................................................ 59 3.3.2 Synthesis of rhodamine methyl- and ethyl ester derivatives.................................................... 65 3.3.3 Dye solutions........................................................................................................................... 68 3.3.4 Cultivation conditions/ Applied dye concentrations................................................................ 69 3.4 Isolation of the diatom cell wall ................................................................................... 70 3.4.1 Sonification.............................................................................................................................. 70 3.4.2 Hot SDS-EDTA-treatment....................................................................................................... 70 3.5 Optical characterization............................................................................................... 71 3.5.1 Absorption- and Fluorescence Spectroscopy........................................................................... 71 3.5.2 Optical Microscopy ................................................................................................................. 71 3.5.3 Fluorescence Microscopy........................................................................................................ 72 3.5.4 Measurement of the fluorescence emission of isolated diatom cell walls: .............................. 73 3.5.5 Confocal Laser Scanning Microscopy (CLSM) ...................................................................... 74 I 3.5.6 Scanning electron microscopy (SEM) ..................................................................................... 74 4 Results and discussion................................................................................................ 75 4.1 In vivo-fluorochromation of diatom cells.................................................................... 75 4.1.1 Biomineralization marker: Rhodamine 123 and LysoSensorTM Yellow/Blue DND-160 ........ 77 4.1.2 Rhodamines ............................................................................................................................