Microarray technology provides a highly sensitive and precise te- nique for obtaining information from biological samples, with the added advantage that it can handle a large number of samples simultaneously that may be analyzed rapidly. Researchers are applying microarray technology to understand gene expression, mutation analysis, and the sequencing of genes. Although this technology has been experimental, and thus has been through feasibility studies, it has just recently entered into widespread use for advanced research. The purpose of DNA Arrays: Methods and Protocols is to provide instruction in designing and constructing DNA arrays, as well as hybridizing them with biological samples for analysis. An additional purpose is to p- vide the reader with a broad description of DNA-based array technology and its potential applications. This volume also covers the history of DNA arrays¿from their conception to their ready off-the-shelf availability¿for readers who are new to array technology as well as those who are well versed in this field. Stepwise, detailed experimental procedures are described for constructing DNA arrays, including the choice of solid support, attachment methods, and the general conditions for hybridization. With microarray technology, ordered arrays of oligonucleotides or other DNA sequences are attached or printed to the solid support using au- mated methods for array synthesis. Probe sequences are selected in such a way that they have the appropriate sequence length, site of mutation, and T .

DNA Microarrays: History and Overview
Edwin M. Southern

Gel-Immobilized Microarrays of Nucleic Acids and Proteins: Production and Application for Macromolecular Research
Jordanka Zlatanova and Andrei Mirzabekov

Sequencing by Hybridization Arrays
Radoje Drmanac and Snezana Drmanac

Ethical Ramifications of Genetic Analysis Using DNA Arrays
Wayne W. Grody

Photolithographic Synthesis of High-Density Oligonucleotide Arrays
Glenn H. McGall and Jacqueline A. Fidanza

Automated Genotyping Using the DNA MassArrayTM Technology
Christian Jurinke, Dirk van den Boom, Charles R. Cantor, and Hubert Köster

Ink-Jet-Deposited Microspot Arrays of DNA and Other Bioactive Molecules
Patrick Cooley, Debra Hinson, Hans-Jochen Trost, Bogdan Antohe, and David Wallace

Printing DNA Microarrays Using the Biomek® 2000 Laboratory Automation Workstation
David W. Galbraith, Jirí Macas, Elizabeth A. Pierson, Wenying Xu, and Marcela Nouzová

Hybridization Analysis of Labeled RNA by Oligonucleotide Arrays
Ulrich Certa, Antoine de Saizieu, and Jan Mous

Analysis of Nucleic Acids by Tandem Hybridization on Oligonucleotide Microarrays
Rogelio Maldonado-Rodriguez and Kenneth L. Beattie

DNA Sequencing by Hybridization with Arrays of Samples or Probes
Radoje Drmanac, Snezana Drmanac, Joerg Baier, Gloria Chui, Dan Coleman, Robert Diaz, Darryl Gietzen, Aaron Hou, Hui Jin, Tatjana Ukrainczyk, and Chongjun Xu

Using Oligonucleotide Scanning Arrays to Find Effective Antisense Reagents
Muhammad Sohail and Edwin M. Southern

Low-Resolution Typing of HLA-DQA1 Using DNA Microarray
Sarah H. Haddock, Christine Quartararo, Patr ick Cooley, and Dat D. Dao

Gene Expression Analysis on Medium-Density Oligonucleotide Arrays
Ralph Sinibaldi, Catherine O'Connell, Chris Seidel, and Henry Rodriguez

Use ofBioinformatics in Arrays
Peter Kalocsai and Soheil Shams

Confocal Scanning of Genetic Microarrays
Arthur E. Dixon and Savvas Damaskinos

Business Aspects of Biochip Technologies
Kenneth E. Rubenstein