BIOTECHNOLOGYINTELLIGENCEUNIT

Integrated Biochipsfor DNA Analysis

Robin Hui Lin, Ph.D.Osmetech Molecular Diagnostics

Pasadena, California, U.S.A.

Abraham P. Lee, Ph.D.University ofCalifornia at Irvine

Irvine, California, U.S.A.

LANDES BIOSCIENCE

AUSTIN, TEXAS

U.S.A.

SPRINGER SCIENCE+BuSINESS MEDIA

NEW YORK, NEW YORK

U.S.A.

INTEGRATED BIOCHIPS FOR DNA ANALYSIS

Biotechnology Intelligence Unit

Landes BioscienceSpringer Science+ Business Media, LLC

ISBN: 978-0-387-76758-1 Printed on acid-free paper.

Copyright ©2007 Landes Bioscience and Springer Science+ Business Media, LLCAll rights reserved.No part of this book may be reproduced or transmitted in any form or by any means, electronic ormechanical, including photocopy, recording, or any information storage and retrieval system, withoutpermission in writing from the publisher.While the authors, editors and publisher believe that drug selection and dosage and the specifications andusageofequipment and devices,as set forth in this book, are in accord with current recommendations andpractice at the time of publication, they make no warranty. expressedor implied. with respect to materialdescribed in this book. In viewof the ongoing research,equipment development, changes in governmentalregulationsand the rapid accumulationofinformation relating to the biomedicalsciences, the reader isurgedto carefullyreviewand evaluatethe information provided herein.

Please address all inquiries to the Publishers:Landes Bioscience, 1002 West Avenue, 2nd Floor, Austin, Texas 78701, U.S.A.Phone: 512/ 637 6050; Fax: 512/ 637 6079www.landesbioscience.com

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Printed in the U.S.A.

9 876 543 2 1

Library ofCongress Cataloging-in-Publication Data

Integrated biochips for DNA analysis / [edited by] Robin Hui Liu, Abraham P. Lee.

p. ; em. -- (Biotechnology intelligence unit)

Includes bibliographical references and index.

ISBN 978-0-387-76758-1

1. DNA microarrays. 2. DNA--Analysis.3. Biochips. I. Liu, Robin Hui. II. Lee, Abra­

ham P. (Abraham Phillip) III. Series: Biotechnology intelligence unit (Unnumbered)

[DNLM: 1. Oligonucleotide Array Sequence Analysis. 2. Sequence Analysis, DNA-­

methods. Q!! 450 1605 2007]

QP624.5.D7261582007

572.8'636--dc22

2007037845

About the Editors...

ROBIN HUI LIU, Ph.D., is the Director ofDevice Technology at OsmetechMolecular Diagnostics (OMD). He received his B.S. degree from South ChinaUniversity of Technology, his M.S. degree from Louisiana Tech University, andhis Ph.D. degree in Mechanical Engineering from University of Il1inois at Urbana­Champaign. Prior to joining OMD, Liu was the Senior Manager of AdvancedTechnology and principal investigator at CombiMatrix Corp. Prior to joiningCombiMatrix, he was a Project Manager at Applied NanoBioscience Center,ArizonaState University (2003), and a Principal Scientist and Group Leader at Motorola Inc.(2000-2003). He was a summer intern at Aclara Biosciences, Inc. (1999). Dr. Liusresearch interests include development of commercial DNA biochip devices andsystems, integrated micro array biochips, microfl.uidic systems for sample preparationand DNA analysis, and integrated immuno-sensors, Dr. Liu is an inventor ofsix USpatents (issued and pending), and the author ofover 30 peer-reviewed papers (in­cludingNatureand PNAS) and four book chapters. He served on the InternationalSteering Committee ofseveral international conferences, including the 26th AnnualInternational Conference of IEEE Engineering in Medicine and Biology Society(Track Chair), the 2nd Annual International IEEE Conference on Microtechnol­ogy, Medicine, and the 2003 International Conference on Materials for AdvancedTechnologies in Singapore. He received two BRAVO awards and 22 Silver QuillAwards from Motorola. He is currently an Associate Editor for the SPIEJournalofMicrolithography, Microfabrication, and Microsystems.

About the Editors...

ABRAHAM P. LEE, Ph.D., is a Professor in the Departments of BiomedicalEngineering (BME) and Mechanical and Aerospace Engineering at the UniversityofCalifornia at Irvine. He is also the associate chair of the BME Department and isthe director the Micro/nano Fluidics Fundamentals Focus (MF3) Center, a DefenseAdvanced Research Projects Agency (DARPA) industry supported research centerthat includes 17 faculty and 17 companies. Prior to joining the U C Irvine faculty in2002, he wasa Senior Technology Advisor in the Office ofTechnology and IndustrialRelations (OTIR) at the National Cancer Institute (NCI) in Bethesda, Maryland,and a program manager in the Microsystems Technology Office (MTO) of theDARPA. While at DARPA, Dr. Lee established the Bio-Fluidic Chips (BioFlips)program and was a founding co-manager of the Fundamental Research at the Bio:Info:Micro Interface program. At LLNL he was a Group Leader with projects onthe treatment ofstroke and CBW defense. Dr. Lee received his Ph.D. (1992) degreein Mechanical Engineering from the University ofCalifornia at Berkeley.ProfessorLee's current research is focused on the development of integrated and "digital"micro/nano fluidics (droplets, pumps, valves,sensors) for the following applications:molecular biosensors to detect environmental and terrorism threats, point-of-carediagnostics, "smart" nanomedicine for early detection and treatment, automatedcell sorting based on electrical signatures, tissue engineering and stem cells, and thesynthesis of ultra-pure materials. He currently serves as Editor for the Journal ofMicroelectromechnical Systems and International Advisory Editorial Board memberofLab ona Chip. Professor Lee has 32 issued US patents and has published over 60peer-reviewed papers in journals and conferences.

Dedication

This book is dedicated to our families.

Dr. Liu's family: Fiona, Vick, Benjamin, Stanley, Shaowen and Zhongji

Dr. Lee's family: Chi, Carmel and Calvin

r.================ CONTENTS ====::=============::::;l

Preface xv

1. Integrated DNA Biochips: Past, Present and Future 1PiotrGrodzimki,RobinHui Liu and AbrahamP.Lee

Early Developments 1Formative years 2New Developments 5Future and Path Forward 7

2. Integrated Molecular Analyses ofBiological Sampleson a Bead-Based Microarray Platform 10JoanneM. Yeakley, DanielA. Peiffer, Marina Bibikoua, Tim McDaniel,

KevinL. Gunderson, RichardSben,Bahram G.Kermani,Lixin Zhou,Eugene Cbudin, Shawn C.Baker, KennethM. Kuhn, FrankSteemers,Mark Hansen, MichaelGraige, Celeste McBride, Steven Barnard,BobKain, David BarkerandJian-Bing FanUniversal Arrays and the GoldenGate® Genotyping Assay 12Gene Expression Analysis with the DASL® Assay 15Allele-Specific Expression Analysis 16DNA Methylation Analysis 17Whole-Genome Gene Expression 19Whole-Genome Genotyping 19

3. Integrated Mierofluidic Customarray" Biochips for Gene Expressionand GenotypingAnalysis 25RobinHui Liu, Mike Lodes, H. SboFuji, DavidDanley

and AndrewMcSheaSemiconductor-Based DNA Microarray 28Microfluidic Cartridge 30Fluidic Architecture and Operation 32Micropumps 32Micromixing .33Microvalves 35Gene Expression Assay 35SubtypingAssay 38Sequencing Assay 40Discussion 41

4. Self-Contained, Fully Integrated Biochips for Sample Preparation,PCRAmplification and DNA Microarray Analysis 46RobinHui Liu, PiotrGrodzimki,Jianing Yangand RalfLenigk

Device Design and Fabrication 48Fluidic Transport 49Micromixing 49Microvalves 52Micropumps 55

Sample Preparation 56On-Chip DNA Amplification 58DNA Microarray Detection 59Pathogenic Bacteria Detection 61Single Nucleotide Polymorphism Assay 62Discussion 62Conclusion 63

5. Integrating Sample Processing and Detection with MicrochipCapillary Electrophoresis ofDNA 68Adam T. Woolley

Microchip CE ofDNA 69Integrating Sample Processing with Microchip CE ofDNA 70Integrated DNA Detectors for CE Microchips 73Phase-Changing Sacrificial Materials for Polymer Microchip

Analysis Systems 73

6. Integrated Plastic Microfluidic Devices for Bacterial Detection 78Z. Hugh Fanand AntonioJ Ricco

Device Design and Fabrication 79Microfluidic Valves 82Screen-Printed Heaters and Electrodes 83PCR 'ThermalCycling 83Bacterial Detection 84

7. PCRin Integrated Microfluidic Systems 90Victor M. Ugaz

PCR in Microfluidic Systems 91Integrated PCR and Gel Electrophoresis 91Integrated PCR and Sample Purification 95Integrated PCR and Hybridization 98Further Advancements in Integration 98Novel Micro-PCR Methods 102

8. Integrated Nucleic Acid Analysis in Parallel Matrix Architecture 107fong Wook Hong

Nucleic Acid Analysis 107Pneumatic Control ofMicrofluid 107Integration and Parallelization on a Microfluidic Chip 108DNA Analyses with Complex Parallelization l09RNA Analyses 111Matrix PCR on a Microfluidic Chip 113Pico Titer Plate-Based PCR 113Microfluidic Digital PCR 114Microfluidic Sanger DNA Sequencing 114

Microfluidic DNA Sequencing-by-Synthesis 115Summary and Perspective 116

9. Chip-Based Genotyping byMass Spectrometry 117KaiTang

MALDI Based GenotypingMethods 119Chip as a Sample Positioning and Concentration Device 120Chip as a Functionalized Capture Device 121ESI Based Genotyping Methods 123

10. Analyzing DNA-Protein Interactions on a Chip 128Limin Lin andJames P. Brody

Approaches to Identify Cis-Regulatory Elements 129Surface Plasmon Resonance-Based Assays 130Using Surface Plasmon Resonance to Measure

DNA-Protein Interaction 131Tests Using a Spreeta Biosensor 132Experimental Set Up 133Measuring DNA-Protein Interactions Using the Surface Plasmon

Resonance Sensor 134Surface Preparation 134Measurements ofDouble-Stranded DNA Surface Adsorption 135Sensitivity ofthe Surface Plasmon Resonance Based Sensor 135Projected Sensitivity Based on Preliminary Experiments 135Surface Plasmon Resonance Is Sensitive Enough to Detect

PhysiologicallyRelevant DNA-Protein Interactions 136

11. Single Molecule DNA Detection 139Tza-HueiWang, Christopher M. Puleo and Hsin-Chih Yeh

Single-Molecule DNA Detection Based on UseofMolecular FRET Probes 141

Single-Quantum-Dot-Based FRET Nanosensor for DNA Detection 142Single-Molecule Fluorescence Burst Coincidence Detection 143Multiplexed DNA Detection Based on Multicolor Colocalization

Analysis ofQuantum Dot Nanoprobes 146Manipulation and Focusing ofSingle Molecules 147Conclusion and Prospectives 147

12. Nanochannels for Genomic DNA Analysis:The Longand the Short ofIt 151RobertRiebn, WalterReisner, JonasO. Tegenfeldt, YanMei Wang;

Chih·kuan Tung, Shuang-FangLim, EdwardCox,jamesC.Sturm,KeithMorton, Steven Y. Chou and RobertH AustinTheory 154Methods: Realizations ofNanochannels 162Experimental Results 165

13. Beyond Microtechnology-Nanotechnology in Molecular Diagnosis ...187Paolo Fortina,joseph Wang, SaulSurrey, jason Y.Park

andLarryJ KrickaHistory ofNanotechnology 187Saferyand Nanotechnology 188Nanofabrication Methods 189Selected Applications in Molecular Diagnosis 190

Index 199

rr================ EDITORS ===================::;-]

Robin Hui LinOsmetech Molecular Diagnostics

Pasadena, California, U.S.A.Email: robin.liu@osmetech.com

Chapters 1, 3, 4

Abraham P.LeeUniversity ofCalifornia at Irvine

Irvine, California, U.S.A.Email: aplee@uci.edu

Chapter 1

11=============CONTRIBUTORS ==============1

Robert H. AustinDepartment ofPhysicsPrinceton UniversityPrinceton. NewJersey, U.S.A.Chapter 12

Shawn C. BakerIllumina, Inc.San Diego, California, U.S.A.Chapter2

David BarkerIllumina, Inc.San Diego, California. U.S.A.Chapter 2

Steven BarnardIllumina, Inc.San Diego, California. U.S.A.Chapter 2

Marina BibikovaIllumina, Inc.San Diego. California, U.S.A.Chapter 2

James P. BrodyDepartment ofBiomedical EngineeringUniversity ofCalifornia at IrvineIrvine . California. U.S.A.Email: jpbrody@uci.eduChapter10

Steven Y.ChouDepartment ofElectrical EngineeringPrinceton UniversityPrinceton, New Jersey, U.S.A.Chapter 12

Eugene ChudinIllumina, Inc.San Diego, California, U.S.A.Chapter 2

Edward CoxDepartment ofMolecular BiologyPrinceton Un iversityPrinceton, New Jersey, U.S.A.Chapter 12

David DanleyCombiMatrix Corp.Mukilteo, Washington, U.S.A.Chapter 3

jian-Bing FanIllumina, Inc.San Diego , California, U.S.A.Chapter 2

Z.HughFanDepartment ofMechanical

and Aerospace EngineeringUniversity ofFloridaGainesville, Florida, US.A.Email: hfan@ufI.eduChapter 6

Paolo FortinaKimmel Cancer CenterThomas Jefferson UniversityPhiladelphia, Pennsylvania, US.A.Email: paolo.fortina@jefferson.eduChapter 13

H. ShoFujiCombiMatrix Corp.Mukilteo, Washington, US.A.Chapter 3

Michael GraigeIllumina, Inc.San Diego, California, US.A.Chapter 2

Piotr GrodzinskiNational Cancer InstituteBethesda, Maryland, US.A.Email: gtodzinp@mail.nih.govChapters 1,4

Kevin L. GundersonIllumina, Inc.San Diego, California, US.A.Chapter 2

Mark HansenIllumina, Inc.San Diego, California, US.A.Chapter 2

Jong Wook HongDepartment ofMechanical EngineeringAuburn UniversityAuburn, Alabama, US.A.Email: jwhong@end.auburn.eduChapter 8

BobKainIllumina, Inc.San Diego, California, US.A.Chapter 2

Bahram G. KermaniIllumina, Inc.San Diego, California, US.A.Chapter 2

Larry J. KrickaDepartment ofPathology

and Laboratory MedicineUniversity ofPennsylvaniaPhiladelphia, Pennsylvania, US.A.Chapter 13

Kenneth M. KuhnIllumina, Inc.San Diego, California, US.A.Chapter 2

RalfLenigkApplied NanoBioscience CenterArizona State UniversityTempe, Arizona, US.A.Chapter 4

Shuang-Fang LimDepartment ofPhysicsPrinceton UniversityPrinceton, New Jersey, US.A.Chapter 12

LiminLinDepartment ofBiomedical EngineeringUniversity ofCalifornia at IrvineIrvine, California, US.A.Chapter 10

Mike LodesCombiMatrix Corp.Mukilteo, Washington, US.A.Chapter 3

Celeste McBrideIllumina, Inc.San Diego, California, U.S.A.Chapter 2

Tim McDanielIllurnina, Inc.San Diego, California, U.S.A.Chapter 2

Andrew McSheaCombiMatrix Corp.Mukilteo, Washington, U.S.A.Chapter 3

Keith MortonDepartment ofElectrical EngineeringPrinceton UniversityPrinceton, NewJersey, U.S.A.Chapter 12

Jason Y. ParkDepartment ofPathology

and Laboratory MedicineUniversity ofPennsylvaniaPhiladelphia, Pennsylvania, U.S.A.Chapter 13

Daniel A. PeifferIllumina, Inc.San Diego, California, U.S.A.Chapter 2

Christopher M. PuleoDepartment ofBiomedical EngineeringJohns Hopkins UniversityBaltimore, Maryland, U.S.A.Chapter 11

Walter ReisnerDepartment ofPhysicsPrinceton UniversityPrinceton, NewJersey, U.S.A.Chapter 12

Antonio J. RiccoNational Center for Space

Biological TechnologiesStanford UniversityStanford, California, U.S.A.Chapter 6

Robert RiehnDepartment ofPhysicsPrinceton UniversityPrinceton, NewJersey, U.S.A.Email: rriehn@ncsu.eduChapter 12

Richard ShenIllumina, Inc.San Diego, California, U.S.A.Chapter 2

Frank SteemersIllumina, Inc.San Diego, California, U.S.A.Chapter 2

James C. SturmDepartment ofElectrical EngineeringPrinceton UniversityPrinceton, NewJersey, U.S.A.Chapter 12

Saul SurreyDepartment ofMedicineThomas Jefferson UniversityPhiladelphia, Pennsylvania, U.S.A.Chapter 13

Kai TangSchool ofBiological SciencesNanyang Technological UniversitySingaporeEmail: tkai@ntu.edu.sgChapter 9

Jonas O. TegenfeldtLund UniversityLund, SwedenChapter 12

Chih-kuan TungDepartment ofPhysicsPrinceton UniversityPrinceton, NewJersey, U.S.A.Chapter 12

Victor M. UgazDepartment ofChemical EngineeringTexas A&M UniversityCollege Station, Texas, U.S.A.Email: ugaz@tamu.eduChapter 7

Joseph WangDepartments ofChemical and Materials

Engineering and ChemistryArizona State UniversityTempe, Arizona, U.S.A.Chapter 13

Tza-Huei WangDepartment ofMechanical EngineeringJohns Hopkins UniversityBaltimore, Maryland, U.S.A.Email: thwang@jhu.eduChapter 11

Yan Mei WangDepartment ofPhysicsPrinceton UniversityPrinceton, New Jersey, U.S.A.Chapter 12

Adam T.WoolleyDepartment ofChemistry

and BiochemistryBrigham Young UniversityProvo, Utah, U.S.A.Email: awoolley@chem.byu.eduChapter 5

Jianing YangApplied NanoBioscience CenterArizona State UniversityTempe, Arizona, U.S.A.Email: jianing.yang@asu.eduChapter 4

Joanne M. YeakleyIllumina, Inc.San Diego, California, U.S.A.Email: jyeakley@illumina.comChapter 2

Hsin-Chih YehDepartment ofMechanical EngineeringJohns Hopkins UniversityBaltimore, Maryland, U.S.A.Chapter 11

LixinZhouIllumina, Inc.San Diego, California, U.S.A.Chapter 2

PREFACE

T he biochip field,fueled by contributors from both academia and industry,has been growing rapidly. DNA biochips are becoming a widespreadtool used in life science, drug screening, and diagnostic applications

due to the many benefits ofminiaturization and integration. The term "DNAbiochip" is used broadly and includes various technologies: DNA microar­rays, microfluidics/Lab-on-a-Chip, and other biochips (such as integratedreal-time PCR, massspectrometry, and nanotechnology-based biochips). Withthe abundance ofgene targets and combinatorial chemistry/biology librariesnow available, researchers have the ability to study the effects of diseases,environmental factors, drugs, and other treatments on thousands ofgenes atonce. Biochips can provide this information in a number ofways, dependingon the type ofchips and chosen design ofthe experiments. They can be used forpharmacogenomics that includes gene expression profiling, the measurementand analysis ofregulated genes under various conditions, and genotyping, thedetection ofpolymorphisms or mutations in a gene sequence. Another majorapplication for DNA biochips is molecular diagnostics, which includes geneticscreening (e.g., detection of mutations or inherited disorders), identificationofpathogens and resistance in infections, and molecular oncology (e.g.,cancerdiagnosis). Biochips can also be used for high-throughput drug screening, foodtesting, chemical synthesis, and many other applications. Drawing steadily onexpertise from engineering, biology, chemistry, and physics, integrated biochipdevices are rapidly becoming sophisticated and affordable.

The objective ofthis book is to provide up-to-date coverageofsome oftheemerging developments in the field of integrated DNA biochips. Chapter 1givesan overviewofthe biochip field,including its history, present developments,and future trends. Chapters 2-4 cover the latest developments in integratedmicro array biochips. In Chapter 2, Yeakleyet al describe a bead-based micro­array platform that has been used in applications ranging from whole genomegenotyping to whole transcriptome expression profiling. In Chapters 3 and 4,focus has been placed on integration ofmicro fluidic technology with micro­arrays.Two different integrated biochip platforms are described: one isdesignedto automate and integrate the microarray process on a chip (Chapter 3) andthe other is capable of performing sample preparation, DNA amplification,microarray hybridization, and electrochemical detection on a single device{Chapter 4).

Chapters 5 and 6 cover the topic of integrated microfluidic capillaryelectrophoresis (CE) biochips that have emerged as an especially promisingapproach for assayinggenetic material. In Chapter 5,Woolley describes some ofthe highly parallel glassmicrochip CE devices and integrated PCR-CE systemsthat were developed by Mathies' group. In Chapter 6, Fan and Ricco detailthe development of integrated plastic microfluidic CE devices that containcomponents for DNA amplification, microfluidic valving, sample injection,on-column labeling, separation, and detection.

Chapter 7 reviewsthe progress that has been made to date in the develop­ment ofmicrofluidic devices capable ofperforming increasingly sophisticatedPCR-based bioassays. In Chapter 8, Hong describes nucleic acid analyses onmicrofluidic chips with particular emphasis on parallel matrix architecture.Several polydimethysiloxane (PDMS)-based integrated systems developed byQuakes group arepresented. In Chapter9,Tang describeschip-based genotypingby mass spectrometry. One ofthe main advantages ofmass spectrometry overother detection methods (e.g., microarrays and CE) is that it provides directreadout of allele types without the need for any labeling. Another label-freedetection technology is a surface plasmon resonance based biosensor that isdescribed in Chapter 10 for identification ofDNA-protein interactions.

The focus ofChapter 11 is on single-molecule detection. Wang et al re­view different technologies for SMD, which has been demonstrated in quantita­tive studies ofboth specific DNA sequences and mutations and can potentiallylead to amplification-free detection ofgenomic DNA. Both Chapters 12 and13 describe the recent development ofnanotechnology used for DNA analysis.In Chapter 12, Riehn et al provide a fairly complete "state ofthe art" report ofhow nanochannels can be used in molecular biology.For example, nanochannelscan be used to analyze genomic length DNA molecules with very high linearspatial resolution. Instead of focusing on a particular nanostructure, Chapter13 gives an overview of various nanotechnologies (including nanoparticles,nanopores, nanochannels, nanowires, nanotubes, etc.) and their applicationsin molecular diagnostics.

Undoubtedly further progress in the integrated DNA biochip field isexpected with the help of microtechnology, nanotechnology, and modernmolecular biology. This book will prove a useful source of information forresearchers in the field ofintegrated DNA biochips and for those who are justentering the field ofbiochip research.

We wish to thank all ofthe contributing authors for their constantly highlevel ofmotivation and enthusiasm and for providing such good manuscripts.We are also thankful to our families (Liu's family including Fiona, Vick,Benjamin, Stanley,Shaowen, and Zhongji; Lee'sfamily including Chi, Carmel,and Calvin) for their patience and support, and for sacrificing precious timethat allowed us to launch into this promising project.

Robin Hui LiuAbraham P. Lee