BioMEMS and Biomedical Nanotechnology Volume II Micro/Nano Technology for Genomics and Proteomics BioMEMS and Biomedical Nanotechnology Mauro Ferrari, Ph.D., Editor-in-Chief Professor, Brown Institute of Molecular Medicine Chairman Department of Biomedical Engineering University of Texas Health Science Center, Houston, TX Professor of Experimental Therapeutics University of Texas M.D. Anderson Cancer Center, Houston, TX Professor of Bioengineering Rice University, Houston, TX Professor of Biochemistry and Molecular Biology University of Texas Medical Branch, Galveston, TX President, the Texas Alliance for NanoHealth Houston, TX Volume II Micro/Nano Technology for Genomics and Proteomics Edited by Mihrimah Ozkan Dept. of Electrical Engineering University of California, Riverside Riverside, California USA Michael J. Heller Dept. of Bioengineering University of California, San Diego La Jolla, California USA Mihrimah Ozkan University of California, Riverside Riverside, California Michael Heller University of California, Riverside Riverside, California Mauro Ferrari Ohio State University Columbus, Ohio Library of Congress Cataloging-in-Publication Data Volume II ISBN-10: 0-387-25564-8 e-ISBN 10: 0-387-25843-4 Printed on acid-free paper. ISBN-13: 978-0387-25564-4 e-ISBN-13: 978-0387-25843-0 Set ISBN-10: 0-387-25661-3 e-ISBN:10: 0-387-25749-7 ISBN-13: 978-0387-25561-3 e-ISBN:13: 978-0387-25749-5 C 2006 Springer Science+Business Media, LLC All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. 987654321 SPIN 11407157 springer.com Dedicated to Richard Smalley (1943–2005), in Memoriam To Rick, father founder of nanotechnology prime inspiration for its applications to medicine gracious mentor to its researchers our light—forever in the trenches with us (Rick Smalley received the 1996 Chemistry Nobel Prize for the co-discovery of carbon-60 buckeyballs) Contents List of Contributors......................................................... xvii Foreword ................................................................... xxi Preface ..................................................................... xxiii I. Application of Microarray Technologies .................................. 1 1. Electronic Microarray Technology and Applications in Genomics and Proteomics ......................................................... 3 Ying Huang, Dalibor Hodko, Daniel Smolko, and Graham Lidgard 1.1 Introduction ......................................................... 3 1.2 Overview of Electronic Microarray Technology ......................... 4 1.2.1 NanoChipr Array and NanoChipr Workstation .................. 5 1.2.2 Capabilities of the NanoChipr Electronic Microarrays............. 7 1.3 Applications ......................................................... 10 1.3.1 Single Nucleotide Polymorphisms (SNPs)—Based Diagnostics ..... 10 1.3.2 Forensic Detection ............................................. 10 1.3.3 Gene Expression Profiling ...................................... 12 1.3.4 Cell Separation ................................................ 12 1.3.5 Electronic Immunoassays ....................................... 14 1.3.6 Miniaturization of Electronic Microarray Technology and Applications ............................................... 15 1.3.7 Applications in Proteomics ...................................... 18 1.4 Summary and Outlook ................................................ 19 References................................................................................. 19 2. Gene Expression Profiling Utilizing Microarray Technology and RT-PCR ........................................................... 23 Dominick Sinicropi, Maureen Cronin, and Mei-Lan Liu 2.1 Introduction ......................................................... 23 2.2 Real-Time PCR . ................................................... 25 2.2.1 Detection Systems.............................................................. 25 2.2.2 Real-Time RT-PCR Data Analysis .......................................... 31 2.2.3 Qualification of Gene Panels Using Real-Time RT-PCR................ 32 2.2.4 Real-Time RT-PCR Summary................................................ 34 viii CONTENTS 2.3 Microarrays.......................................................... 35 2.3.1 Technology Platforms ......................................................... 35 2.3.2 Target Amplification and Labeling.......................................... 37 2.3.3 Applications ..................................................................... 40 2.4 Comparison of Gene Expression Profiling Methods ..................... 41 2.4.1 Comparison of cDNA Arrays with Other Gene Expression Profiling Methods .............................................................. 41 2.4.2 Comparison of Oligonucleotide Arrays with Other Gene Expression Profiling Methods................................................ 42 2.4.3 Comparison of cDNA and Oligonucleotide Microarray Expression Profiles............................................................. 44 2.5 Summary ........................................................... 44 Acknowledgements .................................................................... 45 References ............................................................................... 45 3. Microarray and Fluidic Chip for Extracellular Sensing ................... 47 Mihrimah Ozkan, Cengiz S. Ozkan, Shalini Prasad, Mo Yang, and Xuan Zhang 3.1 Introduction ........................................................ 47 3.2 Antibody Based Biosensors .......................................... 50 3.3 Nucleic Acid Based Biosensors ....................................... 51 3.4 Ion Channel Biosensors .............................................. 51 3.5 Enzyme Based Biosensors ........................................... 51 3.6 Cell Based Biosensors ............................................... 52 3.7 Cellular Microorganism Based Sensors ................................ 52 3.8 Fluorescence Based Cell Biosensors................................... 53 3.9 Cellular Metabolism Based Biosensors ................................ 55 3.10 Impedance Based Cellular Sensors .................................... 56 3.11 Intracellular Potential Based Biosensors ............................... 57 3.12 Extracllular Potential Based Biosensors ............................... 58 3.13 Cell Patterning Techniques ........................................... 60 3.14 Dielectrophoresis for Cell Patterning .................................. 61 3.15 Basis of Dielectrophoresis............................................ 62 3.16 Microelectrodes and Dielectrophoresis ................................ 63 3.17 Dielectric Properties of Cells ......................................... 64 3.18 Effect of Electric Fields on Cells ...................................... 64 3.19 Cell Types and the Parameters for Dielectrophoretic Patterning .......... 65 3.20 Biosensing System . ................................................ 66 3.21 Chip Assembly . .................................................. 66 3.22 Environmental Chamber ............................................. 67 3.23 Experimental Measurement System ................................... 67 3.24 Cell Culture ........................................................ 67 3.24.1 Neuron Culture................................................................ 67 3.24.2 Primary Osteoblast Culture ................................................. 68 3.25 Signal Processing . ................................................. 68 3.26 Selection of Chemical Agents ........................................ 69 CONTENTS ix 3.26.1 Ethanol.......................................................................... 69 3.26.2 Hydrogen Peroxide ........................................................... 69 3.26.3 Pyrethroid ...................................................................... 70 3.26.4 Ethylene Diamene Tetra Acetic Acid (EDTA)........................... 70 3.27 Chemical Agent Sensing ............................................. 70 3.27.1 Signature Pattern for Control Experiments............................... 70 3.28 Electrical Sensing Cycle ............................................. 70 3.29 Ethanol Sensing . .................................................. 71 3.29.1 Single Neuron Sensing....................................................... 71 3.29.2 Single Osteoblast Sensing................................................... 71 3.30 Hydrogen Peroxide Sensing .......................................... 72 3.30.1 Single Neuron Sensing....................................................... 72 3.30.2 Single Osteoblast Sensing................................................... 73 3.31 Pyrethroid Sensing . ................................................. 74 3.31.1 Single Neuron Sensing....................................................... 74 3.31.2