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 .

Includes supplementary material: sn.pub/extras

DNA Microarrays: History and OverviewEdwin M. SouthernGel-Immobilized Microarrays of Nucleic Acids and Proteins: Production and Application for Macromolecular ResearchJordanka Zlatanova and Andrei MirzabekovSequencing by Hybridization ArraysRadoje Drmanac and Snezana DrmanacEthical Ramifications of Genetic Analysis Using DNA ArraysWayne W. GrodyPhotolithographic Synthesis of High-Density Oligonucleotide ArraysGlenn H. McGall and Jacqueline A. FidanzaAutomated Genotyping Using the DNA MassArrayTM TechnologyChristian Jurinke, Dirk van den Boom, Charles R. Cantor, and Hubert KösterInk-Jet-Deposited Microspot Arrays of DNA and Other Bioactive MoleculesPatrick Cooley, Debra Hinson, Hans-Jochen Trost, Bogdan Antohe, and David WallacePrinting DNA Microarrays Using the Biomek® 2000 Laboratory Automation WorkstationDavid W. Galbraith, Jirí Macas, Elizabeth A. Pierson, Wenying Xu, and Marcela NouzováHybridization Analysis of Labeled RNA by Oligonucleotide ArraysUlrich Certa, Antoine de Saizieu, and Jan MousAnalysis of Nucleic Acids by Tandem Hybridization on Oligonucleotide MicroarraysRogelio Maldonado-Rodriguez and Kenneth L. BeattieDNA Sequencing by Hybridization with Arrays of Samples or ProbesRadoje Drmanac, Snezana Drmanac, Joerg Baier, Gloria Chui, Dan Coleman, Robert Diaz, Darryl Gietzen, Aaron Hou, Hui Jin, Tatjana Ukrainczyk, and Chongjun XuUsing Oligonucleotide Scanning Arrays to Find Effective Antisense ReagentsMuhammad Sohail and Edwin M. SouthernLow-Resolution Typing of HLA-DQA1 Using DNA MicroarraySarah H. Haddock, Christine Quartararo, Patr ick Cooley, and Dat D. DaoGene Expression Analysis on Medium-Density Oligonucleotide ArraysRalph Sinibaldi, Catherine O'Connell, Chris Seidel, and Henry RodriguezUse ofBioinformatics in ArraysPeter Kalocsai and Soheil ShamsConfocal Scanning of Genetic MicroarraysArthur E. Dixon and Savvas DamaskinosBusiness Aspects of Biochip TechnologiesKenneth E. Rubenstein