Microarray Technology And Its Applications

by Muller, U. R.; Nicolau, Dan V.

• ISBN13: 9783540229315
• ISBN10: 3540229310
• Format: Hardcover
• Copyright: 2004-12-16
• Publisher: Springer Verlag

Summary

The genomics revolution would not have been possible without the 'parallelisation' offered by microarray technology. This technological - and commercial - success has since been emulated by other applications areas, with a tremendous amplification of innovation. This book describes the fundamentals and latest developments in microarray technology, as well as its future directions. It presents detailed overviews of the different techniques of fabricating microarrays, of the chemistries and preparative steps involved, of the different types of microarrays, and of the instrumentation and optical issues involved.

Table of Contents

Part I General Microarray Technologies
Array Formats	3	(20)
Ralph R. Martel
Matthew P. Rounseville
Ihab W. Botros
Bruce E. Seligmann
Introduction	3	(1)
Reasons to Use Arrays	4	(2)
Arrays for Nucleic Acid Analysis	6	(2)
Protein Arrays	8	(1)
The ArrayPlate™	9	(10)
Conclusion	19	(4)
References	20	(3)
Biomolecules and Cells on Surfaces - Fundamental Concepts	23	(22)
Kristi L. Hanson
Luisa Filipponi
Dan V. Nicolau
Introduction	23	(1)
Types of Immobilization	23	(5)
DNA Immobilization on Surfaces	28	(4)
Protein Immobilization on Surfaces	32	(4)
Carbohydrate Immobilization	36	(2)
Immobilization of Cells on Surfaces	38	(3)
Conclusions	41	(4)
References	42	(3)
Surfaces and Substrates	45	(18)
Alvaro Carrillo
Kunal V. Gujraty
Ravi S. Kane
Introduction	45	(1)
DNA Microarrays	46	(4)
Protein Microarrays	50	(5)
Conclusion	55	(8)
References	56	(7)
Reagent Jetting Based Deposition Technologies for Array Construction	63	(10)
Mitchel J. Doktycz
Introduction	63	(1)
Reagent Jetting -- Technology Overview	63	(2)
Thermal Jet Based Dispensing	65	(2)
Piezo Jet Based Dispensing	67	(1)
Solenoid Jet Based Dispensing	68	(5)
References	71	(2)
Manufacturing of 2-D Arrays by Pin-printing Technologies	73	(16)
Uwe R. Muller
Roeland Papen
Introduction	73	(1)
Definition of `Contact' Pin-Printing	73	(1)
Overview of Different Pin Technologies	74	(5)
Other System Components and Environmental Factors	79	(2)
Pin Printing Process	81	(3)
Example of a High Throughput Pin-Printing System for Manufacturing of 2D Arrays -- the Corning GENII System	84	(2)
Conclusion	86	(3)
References	87	(2)
Nanoarrays	89	(30)
Dan V. Nicolau
Linnette Demers
David S. Ginger
Introduction	89	(2)
Passive Nano-scale Arrays	91	(14)
Computational Nanoarrays	105	(4)
Dynamic Nanoarrays	109	(6)
Conclusion	115	(4)
References	115	(4)
The Use of Microfluidic Techniques in Microarray Applications	119	(28)
Piotr Grodzinski
Robin H. Liu
Ralf Lenigk
Yingjie Liu
Introduction	119	(1)
Biochannel Hybridization Arrays	120	(8)
Chips with Cavitation Microstreaming Mixers -- Kinetics Studies	128	(7)
Integrated Microfluidic Reactors for DNA Amplification and Hybridization	135	(7)
Summary and Conclusions	142	(5)
References	142	(5)
Labels and Detection Methods	147	(34)
James J. Storhoff
Sudhakar S. Marla
Viswanadham Garimella
Chad A. Mirkin
Introduction	147	(1)
Fluorophore Labelling and Detection Methods	148	(3)
Enhanced Fluorescence-Based Assays	151	(3)
Phosphor Reporters	154	(2)
Electrochemical Detection	156	(3)
Metal Nanoparticle Labels and Metal Thin Films for Microarrays	159	(13)
Conclusions	172	(9)
References	174	(7)
Marker-free Detection on Microarrays	181	(30)
Matthias Vaupel
Andreas Eing
Karl-Otto-Greulich
Jan Roegener
Peter Schellenberg
Hans Martin. Striebel
Heinrich F. Arlinghaus
Introduction	181	(1)
Imaging Ellipsometry and Imaging Surface Plasmon Resonance on Biochips	181	(9)
Intrinsic UV Fluorescence for Chip Analysis of Rare Proteins	190	(7)
Genetic Diagnostics with Unlabelled DNA	197	(14)
References	204	(7)
Part II DNA Microarrays
Analysis of DNA Sequence Variation in the Microarray Format	211	(18)
Ulrika Liljedahl
Mona Fredriksson
Ann-Christine Syvanen
Introduction	211	(2)
Principles of Genotyping	213	(4)
Performing the Assays in Practice	217	(5)
Conclusion	222	(7)
References	223	(6)
High Sensitivity Expression Profiling	229	(22)
Ramesh Ramakrishnan
Paul Bao
Uwe R. Muller
Introduction	229	(1)
Oligonucleotide Expression Arrays	230	(9)
cDNA-based Expression Arrays	239	(5)
Appendix	244	(7)
References	245	(6)
Applications of Matrix-CGH (Array-CGH) for Genomic Research and Clinical Diagnostics	251	(14)
Carsten Schwaenena
Michelle Nesslinga
Bernhard Radlwimmera
Swen Wessendorf
Peter Lichtera
Introduction	251	(2)
Technical Aspects	253	(3)
Applications	256	(9)
References	260	(5)
Analysis of Gene Regulatory Circuits	265	(14)
Zirong Li
Introduction	265	(3)
An Experimental Protocol for Genome Wide Location Analysis	268	(5)
Example: Identifying the Target Genes of Human E2F4	273	(2)
Summary	275	(4)
References	275	(4)
Part III Protein Microarrays
Protein, Antibody and Small Molecule Microarrays	279	(18)
Hendrik Weiner
Jorn Glokler
Claus Hultschig
Konrad Bussow
Gerald Walter
Introduction	279	(1)
Protein Microarrays	280	(3)
Antibody Microarrays	283	(4)
Peptide and Other Synthetic Arrays	287	(10)
References	290	(7)
Photoaptamer Arrays for Proteomics Applications	297	(12)
Drew Smith
Chad Greef
Introduction	297	(1)
Overview of Photoaptamer Discovery and High Throughput Production	298	(3)
Using Photoaptamer Microarrays	301	(2)
Discussion	303	(6)
References	305	(4)
Biological Membrane Microarrays	309	(14)
Ye Fang
Anthony G. Frutos
Yulong Hong
Joydeep Lahiri
Introduction	309	(4)
Biospecific Binding Studies Using Membrane Microarrays	313	(5)
Conclusions	318	(5)
References	319	(4)
Part IV Cell & Tissue Microarrays
Use of Reporter Systems for Reverse Transfection Cell Arrays	323	(12)
Brian L. Webb
Introduction	323	(2)
Reporter Systems for Reverse Transfection	325	(7)
Reagents and Protocols	332	(3)
References	333	(2)
Whole Cell Microarrays	335	(10)
Ravi Kapur
Introduction	335	(1)
The Need	336	(1)
The Solution	336	(5)
Challenges and Opportunities for Cellular Microarrays	341	(4)
References	343	(2)
Tissue Microarrays for Miniaturized High-Throughput Molecular Profiling of Tumors	345	(16)
Ronald Simon
Martina Mirlacher
Guido Sauter
Introduction	345	(1)
The TMA Technology	346	(1)
The Representativity Issue	346	(3)
TMA Applications	349	(2)
Future Directions	351	(1)
Protocol	352	(9)
References	354	(7)
Application of Microarray Technologies for Translational Genomics	361	(14)
Spyro Mousses
Natasha Caplen
Mark Basik
Anne Kallioniemi
Olli Kallioniemi
Introduction	361	(2)
High Throughput Clinical Target Validation Using Tissue Microarrays	363	(2)
Examples of Studies Integrating DNA and Tissue Microarray Technologies for the Rapid Clinical Translation of Genomic Discoveries	365	(3)
High Throughput Characterization of Gene Function Using Live Cell Microarrays	368	(2)
Conclusions	370	(5)
References	372	(3)
Index	375