RNA Labeling and Hybridization of DNA Microarrays

DNA array technologies provide powerful tools for comprehensive genomic and transcriptomic exploration in renal research. Applications of DNA arrays include analysis of disease predisposition by using single-nucleotide polymorphism (SNP) microarrays (1 ), reliable detection of chromosomal deletions and amplifications using microarray-based comparative genomic hybridization (array-CGH) (2 ), and global gene-expression patterns by cDNA microarrays (3 ). A DNA microarray consists of a small membrane or glass slide containing samples of many genes arranged in a regular pattern. Genetic content for DNA arrays may consist of cDNA fragments amplified from extensive (EST) clone libraries by high-throughput polymerase chain reaction (PCR) methods. Production of cDNA arrays is error-prone because of requirements for maintenance and processing of large numbers (tens of thousands) of bacterial stock of expressed sequence tag (EST) clones. Synthetic long oligonucleotide probes 45-mer to 70-mer), designed for optimal sequence specificity and annealing temperatures, can be spotted as an alternative to cDNA fragments, and pose lesser logistic and quality-control demands during array production. Ready-to-print oligonucleotide libraries containing probes for human, mouse, or rat Unigene clusters are available from several vendors. Although precise knowledge of exon-specific probe sequences can be a distinct bioinformatics advantage for spotted oligonucleotides, it may pose a considerable problem for genes with extensive alternative splicing of exons.