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Micro-Nano Technology for Genomics and Proteomics BioMEMs - Ozkan

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xii			CONTENTS
	9.4.2 DNA Sequencing ..........................................................		..... 320
	9.4.3 DNA Sample Puriﬁcation ................................................		..... 321
9.5	Protein Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		. . . 322
	9.5.1	Isoelectric Focusing for Studying Protein Interactions .............	..... 323
	9.5.2	Enzymatic Digestion for Protein Mapping ............................	..... 324
	Concluding Remarks..............................................................		..... 326
	Acknowledgements ...............................................................		..... 326
	References ..........................................................................		..... 326
10. Centrifuge Based Fluidic Platforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .			. . . . 329
Jim V. Zoval and M.J. Madou
10.1	Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		. . . 329
10.2	Why Centrifuge as Fluid Propulsion Force? . . . . . . . . . . . . . . . . . . . . . . . .		. . . 330
10.3	Compact Disc or Micro-Centrifuge Fluidics . . . . . . . . . . . . . . . . . . . . . . . .		. . . 333
	10.3.1 How it Works .............................................................		..... 333
10.4 Some Simple Fluidic Function Demonstrated on a CD . . . . . . . . . . . . . .			. . . . 334
	10.4.1	Mixing of Fluid ..........................................................	..... 334
	10.4.2	Valving ....................................................................	..... 335
	10.4.3 Volume Deﬁnition (Metering) and Common
		Distribution Channels ...................................................	..... 338
	10.4.4 Packed Columns .........................................................		..... 339
10.5 CD Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .			. . . . 339
	10.5.1	Two-Point Calibration of an Optode-Based Detection System .	..... 339
	10.5.2 CD Platform for Enzyme-Linked Immunosorbant
		Assays (ELISA) ..........................................................	..... 340
	10.5.3	Multiple Parallel Assays ................................................	..... 341
	10.5.4 Cellular Based Assays on CD Platform ..............................		..... 342
	10.5.5 Automated Cell Lysis on a CD ........................................		..... 344
	10.5.6	Integrated Nucleic Acid Sample Preparation and
		PCR Ampliﬁcation ......................................................	..... 356
	10.5.7 Sample Preparation for MALDI MS Analysis .....................		..... 358
	10.5.8 Modiﬁed Commercial CD/DVD Drives in
		Analytical Measurements ..............................................	..... 359
	Conclusion..........................................................................		..... 361
	Acknowledgements ...............................................................		..... 362
	References ..........................................................................		..... 362
11. Sequencing the Human Genome: A Historical Perspective
On Challenges For Systems Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .			. . . . 365
Lee Rowen
11.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .			. . . . 365
11.2 Approaches Used to Sequence the Human Genome . . . . . . . . . . . . . . . . .			. . . . 366
	11.2.1 Overview...................................................................		..... 366
	11.2.2	Strategy Used for Sequencing Source Clones.......................	..... 368
	11.2.3	Construction of the Chromosome Tiling Paths .....................	..... 379
	11.2.4	Data Sharing ..............................................................	..... 379

CONTENTS			xiii
11.3	Challenges for Systems Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		380
	11.3.1	Methodological Challenges for Sequencing Source
		Clones: 1990–1997 ...........................................................	381
	11.3.2	Challenges for Sequencing the Entire Human
		Genome: 1998–2003..........................................................	386
11.4	Are there Lessons to be Learned from the Human Genome Project? . . . . . .		395
	Acknowledgements ....................................................................		397
	References ...............................................................................		398
III. Nanoprobes for Imaging, Sensing and Therapy . . . . . . . . . . . . . . . . . . . . . . . . . . . .			401
12. Hairpin Nanoprobes for Gene Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .			403
Philip Santangelo, Nitin Nitin, Leslie LaConte, and Gang Bao
12.1	Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		403
12.2	Nanoprobe Design Issues for Homogeneous Assays . . . . . . . . . . . . . . . . . . . .		405
12.3	In Vitro Gene Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		408
	12.3.1	Pathogen Detection ...........................................................	409
	12.3.2	Mutation Detection and Allele Discrimination ..........................	409
12.4	Intracellular RNA Targets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		411
	12.4.1 Cytoplasmic and Nuclear RNA .............................................		411
	12.4.2 RNA Secondary Structure ...................................................		418
12.5	Living Cell RNA Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		418
	12.5.1	Cellular Delivery of Probes..................................................	419
	12.5.2	Intracellular Probe Stability .................................................	424
	12.5.3	Intracellular mRNA Detection ..............................................	428
12.6	Opportunities and Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		431
	Acknowledgements ....................................................................		433
	References ...............................................................................		433
13. Fluorescent Lanthanide Labels with Time-Resolved Fluorometry
In DNA Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .			437
Takuya Nishioka, Jingli Yuan, and Kazuko Matsumoto
13.1	Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		437
13.2	Lanthanide Fluorescent Complexes and Labels . . . . . . . . . . . . . . . . . . . . . . . . .		438
13.3	Time-Resolved Fluorometry of Lanthanide Complexes . . . . . . . . . . . . . . . . .		441
13.4	DNA Hybridization Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		442
	Conclusion...............................................................................		445
	References ...............................................................................		445

14.Role of SNPs and Haplotypes in Human Disease and Drug Development . . 447

Barkur S. Shastry

14.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 447

14.2 SNP Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 448

14.3 Detection of Genetic Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 449

14.4 Disease Gene Mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 450

xiv	CONTENTS
14.5	Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	450
14.6	Haplotypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	452
14.7	Drug Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	452
	Concluding Remarks...................................................................	454
	References ...............................................................................	454
15. Control of Biomolecular Activity by Nanoparticle Antennas . . . . . . . . . . . . . .		459
Kimberly Hamad-Schifferli
15.1	Background and Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	459
	15.1.1 ATP Synthase as a Molecular Motor ......................................	459
	15.1.2 Biological Self Assembly of Complex Hybrid Structures ............	461
	15.1.3 DNA as a Medium for Computation ......................................	463
	15.1.4 Light Powered Nanomechanical Devices .................................	463
15.2	Nanoparticles as Antennas for Controlling Biomolecules . . . . . . . . . . . . . . . .	465
	15.2.1 Technical Approach...........................................................	468
	15.2.2 Dehybridization of a DNA Oligonucleotide Reversibly by
	RFMF Heating of Nanoparticles ...........................................	469
	15.2.3 Determination of Effective Temperature by RFMF
	Heating of Nanoparticles ....................................................	469
	15.2.4 Selective Dehybridization of DNA Oligos by RFMF
	Heating of Nanoparticles ....................................................	471
	Conclusions and Future Work .......................................................	473
	References ...............................................................................	474
16. Sequence Matters: The Inﬂuence of Basepair Sequence
on DNA-protein Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		477
Yan Mei Wang, Shirley S. Chan, and Robert H. Austin
16.1	Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	477
16.2	Generalized Deformations of Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	481
16.3	Sequence Dependent Aspects to the Double Helix Elastic Constants . . . . . .	484
16.4	Sequence Dependent Bending of the Double Helix and the
	Structure Atlas of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	485
16.5	Some Experimental Consequences of Sequence Dependent Elasticity . . . . .	486
	16.5.1 Phage 434 Binding Speciﬁcity and DNase I Cutting Rates ...........	486
	16.5.2 Nucleosome Formation: Sequence and Temperature Dependence ...	491
	Conclusions..............................................................................	494
	References ...............................................................................	494
17. Engineered Ribozymes: Efﬁcient Tools for Molecular
Gene Therapy and Gene Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		497
Maki Shiota, Makoto Miyagishi, and Kazunari Taira
17.1	Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	497
17.2	Methods for the Introduction of Ribozymes into Cells . . . . . . . . . . . . . . . . . . .	498
17.3	Ribozyme Expression Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	499
	17.3.1 The Pol III System ............................................................	499

CONTENTS		xv
17.3.2	Relationship Between the Higher-Order Structure of
	Ribozymes and their Activity ..............................................	500
17.3.3	Subcellular Localization and Efﬁcacy of Ribozymes...................	501
17.3.4 Mechanism of the Export of tRNA-Ribozymes from the
	Nucleus to the Cytoplasm ...................................................	504
17.4 RNA-Protein Hybrid Ribozymes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		505
17.4.1	Accessibility to Ribozymes of their Target mRNAs ....................	505
17.4.2	Hybrid Ribozymes that Efﬁciently Cleave their Target mRNAs,
	Regardless of Secondary Structure ........................................	505
17.5 Maxizymes: Allosterically Controllable Ribozymes . . . . . . . . . . . . . . . . . . . . .		508
17.5.1 Shortened Hammerhead Ribozymes that Function as Dimers ........		508
17.5.2	Design of an Allosterically Controllable Maxizyme....................	509
17.5.3 Inactivation of an Oncogene in a Mouse Model .........................		512
17.5.4 Generality of the Maxizyme Technology ................................		512
17.6 Identiﬁcation of Genes Using Hybrid Ribozymes . . . . . . . . . . . . . . . . . . . . . . .		513
17.7 Summary and Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		515
References ...............................................................................		516
About the Editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .		519
Index . . . . . . . . .	. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .	521

List of Contributors

VOLUME II

Joanna S. Albala, Biology & Biotechnology Research Program, Lawerence Livermore National Laboratory, Livermore, California USA

Robert H. Austin, Dept. of Physics, Princeton University, Princeton, New Jersey USA

Gang Bao, Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia USA

Shirley S. Chan, Dept. of Physics, Princeton University, Princeton, New Jersey USA

Maureen Cronin, Genomic Health, Inc., Redwood City, California USA

Z. Hugh Fan, Dept. of Mechanical and Aerospace Engineering, University of Florida, Gainesville, Florida USA

Mauro Ferrari, Ph.D., 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

Kimberly Hamad-Schifferli, Dept. of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts USA

Michael J. Heller, Dept. of Bioengineering, University of California, San Diego, La Jolla, California USA

Dalibor Hodko, Nanogen Inc., San Diego, California USA

Dr. Ying Huang, Nanogen Inc., San Diego, California USA

Pappanaicken R. Kumaresan, Division of Hematology/Oncology & Internal Medicine, University of California Davis, Sacramento, California USA

xviii

LIST OF CONTRIBUTORS

Leslie LaConte, Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia USA

Kit S. Lam, Division of Hematology/Oncology & Internal Medicine, University of California Davis, Sacramento, California USA

Graham Lidgard, Nanogen Inc., San Diego, California USA

Mei-Lan Liu, Genomic Health, Inc., Redwood City, California USA

Ruiwu Liu, Division of Hematology/Oncology & Internal Medicine, University of California Davis, Sacramento, California USA

M.J. Madou, Dept. of Mechanical and Aerospace Engineering, University of California, Irvine, Irvine, California USA

Jan Marik, Division of Hematology/Oncology & Internal Medicine, University of California Davis, Sacramento, California USA

Kazuko Matsumoto, Dept. of Chemistry and Advanced Research Institute for Science & Engineering, Waseda University, Tokyo, Japan

Makoto Miyagishi, Dept. of Chemistry and Biotechnology, The University of Tokyo, Tokyo, Japan

Takuya Nishioka, Dept. of Chemistry and Advanced Research Institute for Science & Engineering, Waseda University, Tokyo, Japan

Nitin Nitin, Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia USA

Cengiz S. Ozkan, Dept. of Mechanical Engineering, University of California, Riverside, Riverside, California USA

Prof. Mihrimah Ozkan, Dept. of Electrical Engineering, University of California, Riverside, Riverside, California USA

Prof. Ronald Pethig, School of Informatics, University of Wales, Bangor, Gwynedd, United Kingdom

Shalini Prasad, Dept. of Electrical Engineering, University of California, Riverside, Riverside, California USA

Ulrich Reineke, Jerini AG, Berlin, Germany

Antonio J. Ricco, NASA Ames Research Center, Mountain View, California USA

Lee Rowen, Institute for Systems Biology, Seattle, Washington USA

LIST OF CONTRIBUTORS

xix

Philip Santangelo, Dept. of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia USA

Jens Schneider-Mergener, Institut fur¨ Medizinische Immunologie, Universit¨atsklinikum Charit´e, Berlin, Germany

Mike Schutkowski, Jerini AG, Berlin, Germany

Barkur S. Shastry, Dept. of Biological Sciences, Oakland University, Rochester, Michigan USA

Maki Shiota, Dept. of Chemistry and Biotechnology, The University of Tokyo, Tokyo, Japan

Dominick Sinicropi, Genomic Health, Inc., Redwood City, California USA

Daniel Smolko, Nanogen Inc., San Diego, California USA

Kazunari Taira, Dept. of Chemistry and Biotechnology, The University of Tokyo, Tokyo, Japan

Yan Mei Wang, Dept. of Physics, Princeton University, Princeton, New Jersey USA

Mo Yang, Dept. of Mechanical Engineering, University of California, Riverside, Riverside, California USA

Jingli Yuan, Dept. of Chemistry and Advanced Research Institute for Science & Engineering, Waseda University, Tokyo, Japan

Xuan Zhang, Dept of Mechanical Engineering, University of California, Riverside, Riverside, California USA

Jim V. Zoval, Dept. of Mechanical and Aerospace Engineering, University of California, Irvine, Irvine, California USA

Foreword

Less than twenty years ago photolithography and medicine were total strangers to one another. They had not yet met, and not even looking each other up in the classiﬁeds. And then, nucleic acid chips, microﬂuidics and microarrays entered the scene, and rapidly these strangers became indispensable partners in biomedicine.

As recently as ten years ago the notion of applying nanotechnology to the ﬁght against disease was dominantly the province of the ﬁction writers. Thoughts of nanoparticle-vehicled delivery of therapeuticals to diseased sites were an exercise in scientiﬁc solitude, and grounds for questioning one’s ability to think “like an established scientist”. And today we have nanoparticulate paclitaxel as the prime option against metastatic breast cancer, proteomic proﬁling diagnostic tools based on target surface nanotexturing, nanoparticle contrast agents for all radiological modalities, nanotechnologies embedded in high-distribution laboratory equipment, and no less than 152 novel nanomedical entities in the regulatory pipeline in the US alone.

This is a transforming impact, by any measure, with clear evidence of further acceleration, supported by very vigorous investments by the public and private sectors throughout the world. Even joining the dots in a most conservative, linear fashion, it is easy to envision scenarios of personalized medicine such as the following:

patient-speciﬁc prevention supplanting gross, faceless intervention strategies;

early detection protocols identifying signs of developing disease at the time when the disease is most easily subdued;

personally tailored intervention strategies that are so routinely and inexpensively realized, that access to them can be secured by everyone;

technologies allowing for long lives in the company of disease, as good neighbors, without impairment of the quality of life itself.

These visions will become reality. The contributions from the worlds of small-scale technologies are required to realize them. Invaluable progress towards them was recorded by the very scientists that have joined forces to accomplish the effort presented in this 4-volume collection. It has been a great privilege for me to be at their service, and at the service of the readership, in aiding with its assembly. May I take this opportunity to express my gratitude to all of the contributing Chapter Authors, for their inspired and thorough work. For many of them, writing about the history of their specialty ﬁelds of BioMEMS and Biomedical Nanotechnology has really been reporting about their personal, individual adventures through scientiﬁc discovery and innovation—a sort

xxii

FOREWORD

of family album, with equations, diagrams, bibliographies and charts replacing Holiday pictures . . . .

It has been a particular privilege to work with our Volume Editors: Sangeeta Bhatia, Rashid Bashir, Tejal Desai, Michael Heller, Abraham Lee, Jim Lee, Mihri Ozkan, and Steve Werely. They have been nothing short of outstanding in their dedication, scientiﬁc vision, and generosity. My gratitude goes to our Publisher, and in particular to Greg Franklin for his constant support and leadership, and to Angela De Pina for her assistance.

Most importantly, I wish to express my public gratitude in these pages to Paola, for her leadership, professional assistance throughout this effort, her support and her patience. To her, and our children Giacomo, Chiara, Kim, Ilaria and Federica, I dedicate my contribution to BioMEMS and Biomedical Nanotechnology.

With my very best wishes

Mauro Ferrari, Ph.D.

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

Preface

Numerous miniaturized DNA microarray, DNA chip, Lab on a Chip and biosensor devices have been developed and commercialized. Such devices are improving the way many important genomic and proteomic analyses are performed in both research and clinical diagnostic laboratories. The development of these technologies was enabled by a synergistic combination of disciplines that include microfabrication, microﬂuidics, MEMS, organic chemistry and molecular biology. Some of these new devices and technologies utilize sophisticated microfabrication processes developed by the semiconductor industry. Microarrays with large numbers of test sites have been developed which employ photolithography combinatorial synthesis techniques or ink jet type printing deposition methods to produce high-density DNA microarrays. Other microarray technologies have incorporated microelectrodes to produce electric ﬁelds which are able to affect the transport and hybridization of DNA molecules on the surface of the device. As remarkable as this generation of devices and technological appears, the advent of new nanoscience and nanofabrication techniques will lead to even further miniaturization, higher integration and another generation of devices with higher performance properties. Thus, in some sense these devices and systems will follow a similar evolution as did microelectronics in going from 8 bit, to 16 bit to 32 bit technology. Where feature sizes for integrated components of microelectronic devices is now well into the submicron scale, nanoscale biodevices will soon follow. Likewise, the potential applications for this new generation of micro/nanoarray, lab on a chip and nanosensor devices is also broadening into areas of whole genome sequencing, biowarfare agent detection, and remote environmental sensing and monitoring. Today the possibility of making highly sophisticated smart micro/nano scale in-vivo diagnostic and therapeutic delivery devices is being seriously considered.

Nevertheless, considerable problems do exist. Unfortunately, many applications for these bioresearch or biomedically related devices do not have the large consumer markets that will drive and fund their development. The economic forces which drive the development of high volume retail consumer microelectronic and optoelectonic devices (such as computers, cell phones, digital cameras, and ﬁber optic communications), are not there for most bioresearch or biomedical devices. Thus, it is very common to see so-called “good” technologies in the bioresearch and biomedical device area fail somewhere along the arduous path to commercialization. This is particularly true for any biomedical device or system which has to go through the regulatory process. Frequently, the problem relates to the inability to economically manufacture a viable device for commercialization as opposed to a working prototype device. Thus, a key aspect for achieving ﬁnal success for our new

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