Microfluidic Lab-on-a-Chip for Chemical and Biological Analysis and Discovery

DK3682_half-series-title.qxd

8/30/05

12:06 PM

Page A

Microfluidic Lab-on-a-Chip for Chemical and Biological Analysis and Discovery

DK3682_half-series-title.qxd

8/30/05

12:06 PM

Page B

CHROMATOGRAPHIC SCIENCE SERIES A Series of Textbooks and Reference Books Editor: JACK CAZES

1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20.

Dynamics of Chromatography: Principles and Theory, J. Calvin Giddings Gas Chromatographic Analysis of Drugs and Pesticides, Benjamin J. Gudzinowicz Principles of Adsorption Chromatography: The Separation of Nonionic Organic Compounds, Lloyd R. Snyder Multicomponent Chromatography: Theory of Interference, Friedrich Helfferich and Gerhard Klein Quantitative Analysis by Gas Chromatography, Josef Novák High-Speed Liquid Chromatography, Peter M. Rajcsanyi and Elisabeth Rajcsanyi Fundamentals of Integrated GC-MS (in three parts), Benjamin J. Gudzinowicz, Michael J. Gudzinowicz, and Horace F. Martin Liquid Chromatography of Polymers and Related Materials, Jack Cazes GLC and HPLC Determination of Therapeutic Agents (in three parts), Part 1 edited by Kiyoshi Tsuji and Walter Morozowich, Parts 2 and 3 edited by Kiyoshi Tsuji Biological/Biomedical Applications of Liquid Chromatography, edited by Gerald L. Hawk Chromatography in Petroleum Analysis, edited by Klaus H. Altgelt and T. H. Gouw Biological/Biomedical Applications of Liquid Chromatography II, edited by Gerald L. Hawk Liquid Chromatography of Polymers and Related Materials II, edited by Jack Cazes and Xavier Delamare Introduction to Analytical Gas Chromatography: History, Principles, and Practice, John A. Perry Applications of Glass Capillary Gas Chromatography, edited by Walter G. Jennings Steroid Analysis by HPLC: Recent Applications, edited by Marie P. Kautsky Thin-Layer Chromatography: Techniques and Applications, Bernard Fried and Joseph Sherma Biological/Biomedical Applications of Liquid Chromatography III, edited by Gerald L. Hawk Liquid Chromatography of Polymers and Related Materials III, edited by Jack Cazes Biological/Biomedical Applications of Liquid Chromatography, edited by Gerald L. Hawk

DK3682_half-series-title.qxd

8/30/05

12:06 PM

Page C

21. Chromatographic Separation and Extraction with Foamed Plastics and Rubbers, G. J. Moody and J. D. R. Thomas 22. Analytical Pyrolysis: A Comprehensive Guide, William J. Irwin 23. Liquid Chromatography Detectors, edited by Thomas M. Vickrey 24. High-Performance Liquid Chromatography in Forensic Chemistry, edited by Ira S. Lurie and John D. Wittwer, Jr. 25. Steric Exclusion Liquid Chromatography of Polymers, edited by Josef Janca 26. HPLC Analysis of Biological Compounds: A Laboratory Guide, William S. Hancock and James T. Sparrow 27. Affinity Chromatography: Template Chromatography of Nucleic Acids and Proteins, Herbert Schott 28. HPLC in Nucleic Acid Research: Methods and Applications, edited by Phyllis R. Brown 29. Pyrolysis and GC in Polymer Analysis, edited by S. A. Liebman and E. J. Levy 30. Modern Chromatographic Analysis of the Vitamins, edited by André P. De Leenheer, Willy E. Lambert, and Marcel G. M. De Ruyter 31. Ion-Pair Chromatography, edited by Milton T. W. Hearn 32. Therapeutic Drug Monitoring and Toxicology by Liquid Chromatography, edited by Steven H. Y. Wong 33. Affinity Chromatography: Practical and Theoretical Aspects, Peter Mohr and Klaus Pommerening 34. Reaction Detection in Liquid Chromatography, edited by Ira S. Krull 35. Thin-Layer Chromatography: Techniques and Applications, Second Edition, Revised and Expanded, Bernard Fried and Joseph Sherma 36. Quantitative Thin-Layer Chromatography and Its Industrial Applications, edited by Laszlo R. Treiber 37. Ion Chromatography, edited by James G. Tarter 38. Chromatographic Theory and Basic Principles, edited by Jan Åke Jönsson 39. Field-Flow Fractionation: Analysis of Macromolecules and Particles, Josef Janca 40. Chromatographic Chiral Separations, edited by Morris Zief and Laura J. Crane 41. Quantitative Analysis by Gas Chromatography, Second Edition, Revised and Expanded, Josef Novák 42. Flow Perturbation Gas Chromatography, N. A. Katsanos 43. Ion-Exchange Chromatography of Proteins, Shuichi Yamamoto, Kazuhiro Naka-nishi, and Ryuichi Matsuno 44. Countercurrent Chromatography: Theory and Practice, edited by N. Bhushan Man-dava and Yoichiro Ito 45. Microbore Column Chromatography: A Unified Approach to Chromatography, edited by Frank J. Yang 46. Preparative-Scale Chromatography, edited by Eli Grushka 47. Packings and Stationary Phases in Chromatographic Techniques, edited by Klaus K. Unger 48. Detection-Oriented Derivatization Techniques in Liquid Chromatography, edited by Henk Lingeman and Willy J. M. Underberg 49. Chromatographic Analysis of Pharmaceuticals, edited by John A. Adamovics

DK3682_half-series-title.qxd

8/30/05

12:06 PM

Page D

50. Multidimensional Chromatography: Techniques and Applications, edited by Hernan Cortes 51. HPLC of Biological Macromolecules: Methods and Applications, edited by Karen M. Gooding and Fred E. Regnier 52. Modern Thin-Layer Chromatography, edited by Nelu Grinberg 53. Chromatographic Analysis of Alkaloids, Milan Popl, Jan Fähnrich, and Vlastimil Tatar 54. HPLC in Clinical Chemistry, I. N. Papadoyannis 55. Handbook of Thin-Layer Chromatography, edited by Joseph Sherma and Bernard Fried 56. Gas–Liquid–Solid Chromatography, V. G. Berezkin 57. Complexation Chromatography, edited by D. Cagniant 58. Liquid Chromatography–Mass Spectrometry, W. M. A. Niessen and Jan van der Greef 59. Trace Analysis with Microcolumn Liquid Chromatography, Milos KrejcI 60. Modern Chromatographic Analysis of Vitamins: Second Edition, edited by André P. De Leenheer, Willy E. Lambert, and Hans J. Nelis 61. Preparative and Production Scale Chromatography, edited by G. Ganetsos and P. E. Barker 62. Diode Array Detection in HPLC, edited by Ludwig Huber and Stephan A. George 63. Handbook of Affinity Chromatography, edited by Toni Kline 64. Capillary Electrophoresis Technology, edited by Norberto A. Guzman 65. Lipid Chromatographic Analysis, edited by Takayuki Shibamoto 66. Thin-Layer Chromatography: Techniques and Applications: Third Edition, Revised and Expanded, Bernard Fried and Joseph Sherma 67. Liquid Chromatography for the Analyst, Raymond P. W. Scott 68. Centrifugal Partition Chromatography, edited by Alain P. Foucault 69. Handbook of Size Exclusion Chromatography, edited by Chi-San Wu 70. Techniques and Practice of Chromatography, Raymond P. W. Scott 71. Handbook of Thin-Layer Chromatography: Second Edition, Revised and Expanded, edited by Joseph Sherma and Bernard Fried 72. Liquid Chromatography of Oligomers, Constantin V. Uglea 73. Chromatographic Detectors: Design, Function, and Operation, Raymond P. W. Scott 74. Chromatographic Analysis of Pharmaceuticals: Second Edition, Revised and Expanded, edited by John A. Adamovics 75. Supercritical Fluid Chromatography with Packed Columns: Techniques and Applications, edited by Klaus Anton and Claire Berger 76. Introduction to Analytical Gas Chromatography: Second Edition, Revised and Expanded, Raymond P. W. Scott 77. Chromatographic Analysis of Environmental and Food Toxicants, edited by Takayuki Shibamoto 78. Handbook of HPLC, edited by Elena Katz, Roy Eksteen, Peter Schoenmakers, and Neil Miller 79. Liquid Chromatography–Mass Spectrometry: Second Edition, Revised and Expanded, Wilfried Niessen 80. Capillary Electrophoresis of Proteins, Tim Wehr, Roberto Rodríguez-Díaz, and Mingde Zhu

DK3682_half-series-title.qxd

8/30/05

12:06 PM

Page E

81. Thin-Layer Chromatography: Fourth Edition, Revised and Expanded, Bernard Fried and Joseph Sherma 82. Countercurrent Chromatography, edited by Jean-Michel Menet and Didier Thiébaut 83. Micellar Liquid Chromatography, Alain Berthod and Celia García-Alvarez-Coque 84. Modern Chromatographic Analysis of Vitamins: Third Edition, Revised and Expanded, edited by André P. De Leenheer, Willy E. Lambert, and Jan F. Van Bocxlaer 85. Quantitative Chromatographic Analysis, Thomas E. Beesley, Benjamin Buglio, and Raymond P. W. Scott 86. Current Practice of Gas Chromatography–Mass Spectrometry, edited by W. M. A. Niessen 87. HPLC of Biological Macromolecules: Second Edition, Revised and Expanded, edited by Karen M. Gooding and Fred E. Regnier 88. Scale-Up and Optimization in Preparative Chromatography: Principles and Bio-pharmaceutical Applications, edited by Anurag S. Rathore and Ajoy Velayudhan 89. Handbook of Thin-Layer Chromatography: Third Edition, Revised and Expanded, edited by Joseph Sherma and Bernard Fried 90. Chiral Separations by Liquid Chromatography and Related Technologies, Hassan Y. Aboul-Enein and Imran Ali 91. Handbook of Size Exclusion Chromatography and Related Techniques, Second Edition, edited by Chi-San Wu 92. Handbook of Affinity Chromatography, Second Edition, edited by David S. Hage 93. Chromatographic Analysis of the Environment, Third Edition, edited by Leo M. L. Nollet 94. Microfluidic Lab-on-a-Chip for Chemical and Biological Analysis and Discovery, Paul C.H. Li

DK3682_half-series-title.qxd

8/30/05

12:06 PM

Page i

Microfluidic Lab-on-a-Chip for Chemical and Biological Analysis and Discovery

Paul C. H. Li Simon Fraser University Burnaby, British Columbia, Canada

Boca Raton London New York

A CRC title, part of the Taylor & Francis imprint, a member of the Taylor & Francis Group, the academic division of T&F Informa plc.

Dedication To Bosco and Leong Li; Clare, Nickolas and Victoria Provenzano; Edner, Naomi and Hugo Cheng, who may become scientists in the future.

Preface The microfluidic lab-on-a-chip has provided a platform to conduct chemical and biochemical analysis in a miniaturized format. Miniaturized analysis has various advantages such as fast analysis time, small reagent consumption, and less waste generation. Moreover, it has the capability of integration, coupling to sample preparation and further analysis. The book is divided into several chapters which include micromachining methods, microfluidic operations (microfluidic flow, sample introduction, sample preconcentration), chemical separations, detection technology, and various chemical and biochemical analysis (applications on cellular analysis, nucleic acid analysis, and protein analysis). Emphasis will be placed on analytical applications although the basic principles about micromachining and fluid flow and control will also be covered only to the extent that their understanding will assist the exploitation of the microfluidic technology on analytical applications. This book is expanded from a book chapter published in Ewing’s Analytical Instrumentation, edited by Jack Cazes, in 2005. However, the materials have been reorganized to reflect state-of-the-art development. In addition, some errors present in the previous book chapter have been corrected. Beginners in the field should find this book useful to navigate the vast literature of the technology, while experienced researchers will find the compiled information useful for easy comparison and references. Although some comparisons among different approaches are made here, the readers should judge on the suitability of a certain technology for their needs. Moreover, most citations refer to complete studies. Since the field is expanding fast, the proceedings of dedicated conferences, such as Transducers, micro total analysis system (µTAS), will also be cited to include the latest findings. Many of the principles of “operations” on the chip are adapted from conventional wisdom. This adaption not only results in the miniaturization advantage, but also leads to enhanced effects because of favourable scaling down (e.g. plasma emission detection and large DNA molecules separation) and even to scientific discovery (e.g. single-cell study). However, the original citations of these theories or principles, which have already been given in the original research articles, will not be repeated here to avoid increasing the number of microchip references. Therefore, the readers are encouraged to consult the original work from the references cited. The author is indebted to the following individuals without whom this book could not have been realized: Xiujun Li (James) and Wei Xiao who have worked on the references and figures; and Xiujun Li, Alice Koo, Margaret Wong, Maisy Chow, and Wai Lan Chan (Faria), who prepared the text, and Wai Lan Chan (Faria), who also proofread the manuscript.

The Author Dr. Paul Li obtained his M.Sc. and Ph.D on chemical sensors with Professor Michael Thompson in the University of Toronto in 1995. He then worked with Professor Jed Harrison at the University of Alberta during 1995-1996 in the field of microfluidic lab-on-a-chip. During 1996-1998, Dr. Li started his first independent research career at the City University of Hong Kong. After joining Simon Fraser University in 1999, Dr. Li has continued to conduct research in the areas of microfluidics for single-cell analysis. Dr. Li is also interested in integrating microfluidics ith the DNA microarray for pathogen detection and DNA-based diagnostics. He also is interested in analyzing chemical compounds from herbs, especially those with antitumor properties. He has coauthored a book chapter on microfluidic lab-on-a-chip in Ewing’s Analytical Instrumentation Handbook, 3rd edition, 2005.

Contents Chapter 1

Introduction ....................................................................................1

Chapter 2

Micromachining Methods ..............................................................3

2.1

2.2

2.3

2.4

2.5 2.6

Micromachining of Silicon ........................................................................3 2.1.1 Etching of Si Microchannels .........................................................3 2.1.2 Bonding of Si Chips .......................................................................6 Micromachining of Glass .......................................................................... 7 2.2.1 Etching of Glass Microchannels ....................................................8 2.2.2 Drilling of Glass for Access-Hole Formation .............................14 2.2.3 Glass Bonding ..............................................................................16 Micromachining of Fused Quartz (or Fused Silica) ...............................18 2.3.1 Fused Quartz Channel Etching and Hole-Drilling ......................18 2.3.2 Bonding of Fused Quartz Chips ..................................................18 Micromachining of Polymeric Chips .......................................................20 2.4.1 Casting ..........................................................................................20 2.4.2 Injection Molding .........................................................................29 2.4.3 Ablation ........................................................................................30 2.4.4 Wire Imprinting ............................................................................33 2.4.5 Compression Molding ..................................................................34 2.4.6 Photopolymerization .....................................................................37 2.4.7 Other Plastic Micromachining Processes ....................................38 2.4.8 Problems Encountered in Polymeric Chips .................................40 2.4.8.1 Optical Properties ..........................................................40 2.4.8.2 Electrical Properties .......................................................42 2.4.8.3 Thermal Properties .........................................................42 2.4.8.4 Mechanical Properties ....................................................42 2.5.8.5 Surface Properties ..........................................................43 2.4.8.6 Solvent-Resistant Properties ......................................... 45 Metal Patterning .......................................................................................46 World-to-Chip Interface .......................................................................... 49

Chapter 3

Microfluidic Flow .........................................................................55

3.1

Pumping Methods ........................................................................55 Electroosmotic Flow (EOF) .........................................................55 Pressure-Driven Flow ...................................................................56 Centrifugal Pumping ....................................................................57 Alternative Pumping Principles ...................................................59

Liquid 3.1.1 3.1.2 3.1.3 3.1.4

3.2

3.1.4.1 EOF-Induced Flow .........................................................59 3.1.4.2 Electrochemical Bubble Generation ..............................59 3.1.4.3 Thermally Induced Pumping .........................................63 3.1.4.4 Surface Energy ...............................................................65 3.1.4.5 Pneumatic Control......................................................... 65 3.1.4.6 Magnetohydrodynamic (MHD) Pumping .....................65 3.1.4.7 Evaporation ....................................................................66 3.1.4.8 Miscellaneous Pumping Methods................................. 66 3.1.5 Microfluidic Flow Modeling Study .............................................67 Microfluidic Flow Control .......................................................................68 3.2.1 Surface Modifications for Flow Control ......................................68 3.2.2 Laminar Flow for Liquid Extraction and Microfabrication ........72 3.2.3 Generation of Concentration and Temperature Gradients ...........76 3.2.4 Flow Switching ............................................................................79 3.2.5 Fluid Mixing .................................................................................90 3.2.5.1 Diffusive Mixing ............................................................91 3.2.5.2 Chaotic Advection ..........................................................91 3.2.5.3 Oscillating Flow ............................................................ 95 3.2.5.4 Acoustic Mixing ............................................................96 3.2.5.5 Other Mixing Methods ..................................................98 3.2.6 Liquid Dispensing ........................................................................99

Chapter 4 4.1

4.2 4.3

Electrokinetic Injection ..........................................................................103 4.1.1 Pinched Injection ........................................................................107 4.1.2 Gated Injection ...........................................................................115 Hydrodynamic Injection .........................................................................117 Other Sample Injection Methods ...........................................................121

Chapter 5 5.1 5.2 5.3 5.4

Sample Pre-Concentration .........................................................123

Sample Stacking .....................................................................................123 Extraction ...............................................................................................125 Porous Membrane ..................................................................................129 Other Pre-Concentration Methods .........................................................137

Chapter 6 6.1 6.2

Sample Introduction ...................................................................103

Separation ...................................................................................141

Gas Chromatography (GC) ....................................................................141 Capillary Electrophoresis (CE) 1 ............................................................143 6.2.1 Free-Solution Capillary Electrophoresis (FSCE) ......................143 6.2.2 Capillary Gel Electrophoresis (CGE) ........................................151 6.2.3 Micellar Electrokinetic Capillary Chromatography (MEKC) ....155 6.2.4 Isotachophoresis (ITP) ...............................................................158

6.2.5 6.2.6 6.2.7 6.2.8

6.3 6.4

Capillary Electrochromatography (CEC) ..................................160 Synchronized Cyclic Capillary Electrophoresis (SCCE) ..........166 Free-Flow Electrophoresis (FFE) ...............................................170 Derivatizations for CE for Separations ......................................171 6.2.8.1 Pre-Column Derivatization ..........................................171 6.2.8.2 Post-Column Derivatization .........................................174 Chromatographic Separations ................................................................175 Coupled Separations ...............................................................................176 6.4.1 Fraction Collection .....................................................................176 6.4.2 Two-Dimensional Separations ...................................................179

Chapter 7 7.1

7.2

7.3

7.4

Detection Methods .....................................................................187

Optical Detection Methods ....................................................................187 7.1.1 Fluorescence Detection ..............................................................187 7.1.1.1 Single-Channel Fluorescence Detection ......................187 7.1.1.2 Scanning Detector ........................................................190 7.1.1.3 Background Reduction ................................................191 7.1.1.4 Photobleaching Effect ..................................................192 7.1.1.5 Integrated Fluorescent Detector ...................................193 7.1.2 Indirect Fluorescent Detection ...................................................195 7.1.3 Multiple-Point Fluorescent Detection ........................................196 7.1.4 Absorbance Detection ................................................................200 7.1.5 Plasma Emission Detection ........................................................202 7.1.6 Chemiluminescence (CL) Detector ............................................205 7.1.7 Refractive Index (RI) .................................................................208 7.1.8 Thermal Lens Microscope (TLM) .............................................209 7.1.9 Raman Scattering .......................................................................210 7.1.10 Surface-Plasmon Resonance ......................................................211 7.1.11 Infrared Detection ......................................................................211 Electrochemical (EC) Detection .............................................................211 7.2.1 Amperometric Detection ........................................................... 212 7.2.2 Voltammetric Detection ..............................................................218 7.2.3 Potentiometric Detection ............................................................220 7.2.4 Conductivity Detection ..............................................................220 Mass Spectrometry (MS) .......................................................................224 7.3.1 Electrospray Ionization (ESI) ....................................................224 7.3.2 Matrix-Assisted Laser Desorption Ionization (MALDI) ...........235 Other Detection Methods .......................................................................238 7.4.1 Thermal Detection ......................................................................238 7.4.2 Acoustic Wave Detection ...........................................................246 7.4.3 Nuclear Magnetic Resonance (NMR) .......................................247

Chapter 8 8.1

8.2 8.3

Retention of Cells and Particles ............................................................251 8.1.1 Slit-Type Filters ..........................................................................251 8.1.2 Weir-Type Filters ........................................................................255 8.1.3 Cell Adhesion .............................................................................263 8.1.4 Polymer Entrapment ...................................................................267 8.1.5 Three-Dimensional Flow Control ..............................................269 8.1.6 Optical Trapping of Cells ...........................................................273 8.1.7 Dielectrophoresis (DEP) ............................................................277 Studies of Cells in a Flow .....................................................................280 Other Cell Operations ............................................................................288 8.3.1 Cell Culture ................................................................................288 8.3.2 Electroporation .......................................................................... 290 8.3.3 Chip Cleaning and Sterilization .................................................292 8.3.4 Prevention of Cell Adhesion ......................................................292

Chapter 9 9.1 9.2

9.3

9.4

Applications to Cellular/Particle Analysis ..................................251

Applications to Nucleic Acids Analysis ....................................293

Nucleic Acids Extraction and Purification ............................................293 Nucleic Acids Amplification ..................................................................294 9.2.1 DNA Amplification ....................................................................294 9.2.1.1 Polymerase Chain Reaction (PCR) .............................294 9.2.1.2 Surface Passivation of PCR Chambers .......................301 9.2.1.3 Integrated DNA Analysis Microsystems .....................301 9.2.1.4 Real-Time PCR ........................................................... 306 9.2.1.5 Flow-Through PCR ......................................................309 9.2.1.6 Other DNA Amplification Techniques ........................310 9.2.2 RNA Amplification ....................................................................311 DNA Hybridization ................................................................................313 9.3.1 Microchannel DNA Hybridization .............................................313 9.3.2 Microarray DNA Hybridization .................................................317 Other Nucleic Acid Applications .......................................................... 317 9.4.1 DNA Sequencing ........................................................................317 9.4.2 Genetic Analysis .........................................................................320 9.4.3 Separation of Large DNA Molecules ........................................325

Chapter 10 Applications to Protein Analysis ...............................................337 10.1 Immunoassay ..........................................................................................337 10.1.1 Homogeneous Immunoassay .....................................................337 10.1.2 Heterogeneous Immunoassay .....................................................343 10.2 Protein Separation ..................................................................................349 10.3 Enzymatic Assays ...................................................................................353 10.3.1 Assay of the Enzymes ................................................................353 10.3.2 Assay of Analytes after Enzymatic Reactions ..........................358

Appendix ..........................................................................................................365 Problem Sets ....................................................................................................393 1 Introduction ............................................................................................393 2 Micromachining .....................................................................................393 3 Microfluidic Flow ...................................................................................395 4 Sample Introduction ...............................................................................396 5 Sample Pre-concentration...................................................................... 396 6 Separation ...............................................................................................397 7 Detection .................................................................................................397 8 Cellular Analysis ....................................................................................400 9 Nucleic Acid Analysis ............................................................................400 10 Protein Analysis .....................................................................................401 References ........................................................................................................403 Glossary ...........................................................................................................477 Index .................................................................................................................487

1 Introduction A miniaturized gas chromatographic (GC) column with a thermal conductivity detector (TCD) on silicon (Si) was first constructed in 1979 [1] and an HPLC column with a conductometric detector was constructed on Si–Pyrex in 1990 [2]. The first demonstration of a liquid-based miniaturized chemical analysis system was based on CE, and this appeared in 1992 [3]. In this work, CE separation of calcein and fluorescein as detected by LIF was achieved on a glass chip with a 10-µm-deep and 30-µm-wide channel in 6 min. The success is attributed to the use of electroosmotic flow (EOF) to pump reagents inside small capillaries which could develop high pressure, preventing the use of HPLC. Since then, different CE modes have been demonstrated and different analyses (i.e., cellular, oligonucleotide, and protein analyses) have been achieved by numerous research groups, as mentioned in subsequent sections. In this book, we focus on the microfluidic lab-on-a-chip (coined in 1992) [582] which consists of the micromachined channels and chambers. Other important chip-based technology such as microarray or microwells is beyond the scope of this book. Applications other than analysis, such as chemical synthesis, which have been reviewed recently [4], are not covered here either. Recently, numerous review articles summarizing research performed in the area of the microfluidic chip have been published [5,6]. Reviews on specific topics have also appeared (see Table 1.1). Whereas these reviews summarize exciting research and propose new directions, this book is focused on an overview of the available technology, its limitations, and its breakthroughs over the years. TABLE 1.1 Reviews on Microfluidic Chip Technology Review Topics History Miniaturization µTAS Separation Clinical analysis Cellular analysis Protein analysis Nucleic acids analysis Detector Sample introduction Microfabrication Microfluidic flow Micropumps Microvalves Micromixers

5, 5, 5, 6, 6, 6, 4, 6, 6, 6, 5, 5, 5, 5, 6,

References 7–11 12–17, 19, 21, 31 8, 11, 16, 18–25 9, 21, 26–34, 44, 46, 47, 53, 189 35–40 40–43, 73 6, 42, 44–50 36, 42, 44, 45–47, 49, 51–59 8, 44, 46, 53, 60–70 8, 10, 32, 65, 71 7, 8, 26, 42, 44, 72–78, 189 10, 18, 39, 52, 53, 79 8, 11, 18, 21, 23, 80–82 11, 18, 21, 23, 80–82 11, 80

1

2 Micromachining Methods Micromachining methods, which include film deposition, photolithography, etching, access-hole drilling, and bonding of microchip, were first achieved on silicon (Si) [3]. Thereafter, glass (Pyrex glass, soda lime glass, fused silica) was used as the micromachining substrate. Recently, polymeric materials have become widely used as substrates. The micromachining methods of these substrates differ and are given in separate subsequent sections.

2.1 MICROMACHINING OF SILICON The Si substrate was micromachined based on photolithography; see Figure 2.1 for the process steps of a standard one-mask Si-micromachining process [3]. After photolithography, the exposed portions of photoresist were dissolved by a developer, and the remaining unexposed areas were hardened by heating (baking). The exposed areas of the Si substrate were etched subsequently. Meanwhile, a Pyrex glass plate was patterned with metal electrodes. Then the Pyrex plate was bonded to the Si wafer using the anodic bonding process. The etching, access-hole drilling, and bonding processes are described in more detail in subsequent sections.

2.1.1 ETCHING

OF

SI MICROCHANNELS

Isotropic wet etch using HF-HNO3, whose etch rate is independent of the etching direction, has been employed to produce approximately rectangular grooves, oriented in any direction on the Si wafer, using thermal SiO2 (∼ 1 µm thick) as the etch mask [1]. Anisotropic etch, whose etch rate depends on the etching direction, can be achieved using KOH on Si or Si. This method allows V-grooves or vertical walls to be formed on the substrate. Apparently, the anisotropic etch rate of Si at the crystal plane was very small in comparison with the plane [827]. Therefore, the etch depth will be dependent on the opening width, rather than the etch time. However, this method will produce the desired groove profiles only if the groove lies along specific crystallographic axes on the wafer, and certain shapes (square corner and circle) cannot easily be realized [1], except by corner compensation [281]. In Figure 2.2, anisotropic KOH etch on Si will produce a rectangular cross section, if the channel is 45° relative to the wafer flat (A–A′, B–B′, and

3

4

Microfluidic Lab-on-a-chip for Chemical/Biological Analysis and Discovery Polished Si wafer Thermal oxide deposition

Si SiO2 Photoresist

Photoresist deposition Light Mask Photolithography

Developing

Etching the oxide

Removing the photoresist Etching the Si microstructure Structured Si wafer

FIGURE 2.1 Process steps of a standard one-mask micromachining procedure to etch a channel structure into silicon [3]. Reprinted with permission from Elsevier Science.

C–C′). But if the channel is perpendicular to the wafer flat (D–D′), a V-groove cross section will result due to the slanted planes that define the stop-etch conditions [84]. Isopropyl alcohol (IPA) is sometimes added to KOH in order to reduce the etchant surface tension. This in turn assists in releasing H2 bubbles and in dissolving organic contaminants. So the addition of IPA avoids the micromask effect and produces smoothly etched channels [303]. Anisotropic etch on Si can also be achieved by reactive ion etching (RIE), which is a dry (plasma) etch process. In deep RIE, cyclic etch characteristics could be produced on the etched wall [85,86]. Different etch methods used to produce microfluidic chips on Si are tabulated in Table 2.1.

Micromachining Methods

5

B′ B D

A I

D′

A′ C II

C′

FIGURE 2.2 Microstructures defined on a silicon wafer for chemical separation. Design I–cross-type separator; Design II–45° type separator [84]. Reprinted with permission from the Royal Society of Chemistry.

TABLE 2.1 Etching of Si Substrates Etch Conditions HF-HNO3

TMAH and water (1:4), EDP

KOH with IPA

KOH

RIE DRIE (SF6 plasma)

Etch Results Isotopic Wet Etch Unspecified etch rate

References 1

Anisotropic Wet Etch 28 µm in 30 min (90°C) 175 µm (∼ 80°C) 100 µm/h 43 µm in 100 min, 98°C 2.5 µm/min, 115°C Unspecified etch rate ∼ 0.4 µm/min10% IPA,76°C 3% IPA, 70°C 5% IPA, 60°C 380 µm in 4–5 h, 85°C ∼36 µm/h, 70°C 17 µm, 75°C Unspecified etch rate

856 299 90, 390 1011 300 301 302 303 223 304 215 209 1, 213, 249, 305, 825

Anisotropic Dry Etch Unspecified etch rate 5 µm/min 2–3 µm/min Unspecified etch rate

85, 307, 458, 459, 825 860 308, 309 847

6

Microfluidic Lab-on-a-chip for Chemical/Biological Analysis and Discovery

Since Si is a semiconductor, it is not electrically insulating. However, electrical insulation (< 500 V) of Si can be provided by a film of SiO2/Si3N4 (∼ 200 nm) [304] or low-temperature oxide (LTO) [87]. It was found that insulation by the SiO2 film was better achieved by plasma deposition rather than by thermal growth; a 13-µm thick plasma-deposited SiO2 film would withstand an operation voltage of 10 kV [88,706]. For better insulating properties, glass (e.g., Pyrex, fused silica), which sustains at least an electric field of 105 V/cm without dielectric breakdown, is used. After etching, access holes can be created on the Si substrate by wet etchthrough [1,89,90,281,306] or by drilling [442,495]. A two-mask process was also used to create channel access holes on the Si wafers [90].

2.1.2 BONDING

OF

SI CHIPS

Anodic bonding of Si to Pyrex was commonly used to create a sealed Si chip [1,281,442,820,836]. Various bonding conditions used are summarized in Table 2.2. A positive voltage is applied on the Si wafer with respect to that of the Pyrex wafer (negative) [91,92,281]. If anodic bonding between glass and Si fails (due to a thick oxide layer [1 µm] on Si or platinum electrode on Si), a low-melting spin-on-glass (SOG) can be applied as an adhesive. SOG, which is a methylsilsesquioxane polymer, flows very well at the temperature between 150°C and 210°C, and therefore it fills the grooves (i.e., around the Pt electrodes) for effective bonding [93]. Bonding of Si to glass was also achieved using UV-curable optical adhesives. Benzocyclobutene has been used to bond Si and Pyrex [94–99,942].

TABLE 2.2 Various Conditions of Anodic Bonding of Si and Pyrex Plates Temperature 200–300°C 350°C 375°C 400°C

430°C 450°C

485°C

Voltage 200–400 V 1100 V 2–5 min 700 V (under N2 at atmosphere pressure) 1000–1500 V for 30 min 400 V 600 V 800 V 1600 V for 40 min 1600 V 800 V 850 V 1000 V 800 V

References 91 304 310 309 390 1 820 308 306, 311 92 312 281, 299 90

Micromachining Methods

7

On the other hand, bonding of Si to Si was achieved by a low-temperature curing polyimide film [100], or by using an intermediate deposited layer of borophosphosilicate glass and subsequent anodic bonding (300 V, 350°C) [101].

2.2 MICROMACHINING OF GLASS Similar to the procedure for Si micromachining, micromachining for glass also includes thin-film deposition, photolithography, etching, and bonding (see Figure 2.3) [102].

Cr & Au

Photoresist

(a)

Glass

UV light Mask Glass

Glass

Glass

(b)

(c)

(d)

(e) Glass

Glass

(f )

Glass (g) Glass

FIGURE 2.3 Sequence for fabrication of the glass microfluidic chip. (a) Cr and Au masked glass plate coated with photoresist; (b) sample exposed to UV light through a photomask; (c) photoresist developed; (d) exposed metal mask etched; (e) exposed glass etched; (f) resist and metal stripped; (g) glass cover plate bonded to form sealed capillary [102]. Reprinted with permission from American Chemical Society.

8

Microfluidic Lab-on-a-chip for Chemical/Biological Analysis and Discovery

2.2.1 ETCHING

OF

GLASS MICROCHANNELS

Etching of glass is commonly achieved by isotropic wet etch. Various etching conditions based on HF are tabulated in Table 2.3. A typical glass channel created by wet etch is shown in Figure 2.4. The etch rate of Pyrex depends on the HF concentration. The lateral etch rate was found to be greater than the vertical etch rate, and the rates were reduced from 12 to 0.5 µm/min when the HF concentration decreased from 49% to 25%. Before photolithography, a photoresist film is usually spin-coated on glass. To improve the adhesion of photoresist on glass, it is first spin-coated with a film of hexamethyldisiazane. On the other hand, to coat photoresist on glass plates with holes, the glass should be dip-coated [103–105]. In the photolithographic process, a photomask is needed. The photomask is usually generated by photoablation (by a laser) or e-beam ablation. It is found that e-beam ablation has produced smoother edges (10 times better than the UV laser-ablated mask) in the photomask, thus leading to smoother channel walls after etching, and higher efficiency in CE separations [106]. Uniformity in channel depth and width can be experimentally verified by examining the linearity of a plot of separation efficiency (N) versus channel length (L) [107]. Scratch effects in glass etch can be reduced by pre-etching the glass in HF before deposition of the metal etch mask [108]. For mechanically polished glass plates, thermal annealing should be performed before etching to improve etch quality [96,102,105,109,430,529]. To improve channel smoothness, wet HF etch was performed in an ultrasonic bath [105,529,626] or wafted by hand [136]. The glass being etched was also agitated every 10 min for 2–3 h, followed by lateral stirring with a plastic rod [110,136]. Borofloat glass does not require agitation during HF etch and leaves no reaction products as is seen with soda lime glass [108]. In one report, surfactant was added to yield better dimensional consistency and smoothness of channel edges [626]. In another case, glycerol was added to the HF etching bath [729]. To remove precipitated particles in the BOE process, the substrates were removed every 2–5 min and dipped in a 1 M HCl solution for 10–20 s. Adding HCl directly into the HF etch bath will have a similar effect [105,109–111]. Because wet chemical etch on glass results in an isotropic etch, the resulting channel cross section is trapezoidal or semicircular [112,136,137]. In order to form a circular channel, two glass plates were first etched with a mirror image pattern of semicircular cross section channels. Then the two plates were aligned and thermally bonded to form a circular channel [113,114,456,802,813]. Normally, a one-mask process was employed for glass etching, but for specific applications, a two-mask process was used to create the shallow channel (1–6 µm deep) and the deep channel (20–22 µm deep) [115,117]. In order to fabricate shallow (18 µm) and deep (240 µm) glass channels, they were etched separately on the bottom and top plates using two masks. Alignment was achieved during bonding

Micromachining Methods

9

TABLE 2.3 HF-Based Wet Etching of Glass Etch Conditions BOEa (10:1) BOE (7:1) BOE (6:1)

BOE (unspecified ratio) 32% HF/NH4F (1:1) HF/NH4F (1.7%:2.3%) 5% NH4Cl/1% HF HF (1%)/NH3 Conc. HF

50% HF

49% HF

25% HF 20% HF 10% HF

50% HF/H2O (1:5) HF/HNO3 (7:3) HF/HNO3 HF/HNO3/H2O (20:14:66)b

5% HF/70% H3PO4 HF/HCl/H2O (1:1:2)

Etch Results ∼ 10 nm/min Unspecified etch rate 0.03 µm/min 0.9 µm/min 36 µm in 40 min 10 µm in 20 min 0.66 µm/min Unspecified etch rate 8 µm in 15 min

References 302 102 313 314 105 103 747 110, 447, 529 315

5.2 µm in 20 min (stirred) 2 µm/min ∼ 0.7 µm/min

316, 317, 564 125 318

Unspecified etch rate Unspecified etch rate 100 µm in 1 h (70°C) 30 µm in 4 min 20 µm for 3 min 7 µm/min ∼ 10 µm/min 13 µm/min ∼ 8 µm/min 9 µm/min 7 µm/min

273 136 284 980 610 114 1017 319, 430 615 313 95, 96, 98, 244, 320, 409, 536, 548, 557 739 321 92 125

30 µm for 15 min Unspecified etch rate ∼ 1.1 µm/min (21°C) With flow (1.55 µm/min soda lime glass, 0.786 µm/min borosilicate); no flow (0.85 µm/min (soda lime) 12.9 µm/h 6.5 µm/min Unspecified etch rate 25 µm in 6 min 2 µm/min 0.8 µm/min ∼ 0.3 µm/min Unspecified etch Unspecified etch 16 µm/2.5 min Unspecified etch Unspecified etch

rate rate

122 322, 323, 394 324, 330, 844 818 117 325 139 102, 292, 326, 327, 1078 145, 328 329 244, 282 670

rate BOE (6:1)/HCl/H2O rate (1:2:4) aBOE represents buffered oxide etch with various ratios of 40% NH F/49% HF. 4 bHF/HNO /H O(20:14:66) is identical to 49% HF/69%HNO /H O (2:1:2). 3 2 3 2

10

Microfluidic Lab-on-a-chip for Chemical/Biological Analysis and Discovery

FIGURE 2.4 Electron micrograph of a T-intersection on a Pyrex glass microchip [102]. Reprinted with permission from the American Chemical Society.

[116,117]. Two-level glass etch was also performed first over photoresist for shallow etch (10 µm), and then over black lithographical masking tape for deep etch [117]. It was reported that double etch (shallow + deep etch) resulted in a cross section leading to less dispersion in chemical separations (by simulation) than the usual single deep-etched cross section [118,119]. Channel etching using HF was usually performed before bonding, but etching could also be achieved after glass bonding (for enlarging some channels) [120,121,671,1065]. Deep wet HF etch of borosilicate glass to > 500 µm depth was achieved. This was carried out using an anodically bonded Si wafer (patterned) as a mask. Conventional Cr/Au etch mask can only produce shallow etch (< 50 µm) before the problem of pinholes appeared. After etching, the Si mask was sacrificed by KOH etching, thus releasing the etched glass plate. The glass plate could then be sealed with a Si cover plate by anodic bonding for a second time [122]. In the selection of etch mask for deep glass etching, thick SU-8 is a choice, but SU-8 cannot be used in a HF bath (48%) because SU-8 does not adhere well to SiO2 [123]. However, with a polycrystalline amorphous Si seed layer SU-8 adheres very well. For instance, with a 1.5-µm-thick polished polysilicon, a 50µm-thick SU-8 can be deposited as the etch mask, leading to a maximum etch depth of 320 µm. Usually photoresist (2 µm thick) is only useful for shallow etch, less than 50 µm [123]. Polished or unpolished polysilicon (by low-pressure CVD at 620°C) is another etch mask option. Utilizing 2.5-µm-thick unpolished polysilicon, a maximum etch depth of 160 µm was reached using a HF/H2O/HNO3 (6:40:100) solution. Further etching causes large pits (1.5–2.2 mm dia.) to form on the glass. With polished polysilicon (1.5 µm thick), etch depth up to 250 µm can be achieved. When amorphous Si is used as the etch mask, a maximum etch depth of 170 µm can be reached [123].

Micromachining Methods

11

Deep-glass etching is useful in creating special glass structures such as a glass diaphragm. Forturan is another glass material used to make chips. When treated in a high-temperature oven (500°C for 1 h and then 600°C for 1 h), the exposed regions on the Forturan wafer will be transformed into a ceramic which has a much higher etch rate (e.g., in 10% HF) than the surrounding glass [124]. Instead of photolithography, glass chips have been patterned using the PDMS channel mask. Glass etching can be achieved directly in the regions defined by PDMS channels. On the other hand, glass etching is achieved using an etch mask (Ni) which is formed by electrodeless deposition in the regions as defined by the PDMS channels. Wet HF etch or dry plasma etch has been carried out on soda lime glass (microscope slides) or borosilicate glass (coverslips) [125]. Dry etch of glass by RIE has also been reported [813]. Figure 2.5 shows the comparison of wet etch (10% HF) in two types of glass using PDMS channels for patterning.

8

Depth/+m

0