Theoretical considerations for the efficient design of dna arrays

The use of combinatorial or array-based detection (and synthesis) technologies has qualitatively changed many areas of bioscience in the last several years. These technologies include DNA, protein, and combinatorial chemistry arrays. Of these, DNA arrays, designed to determine gene content and expression levels in living cells, have shown the most potential. DNA arrays allow simultaneous, parallel measurement of thousands of interactions between target strands and genome-derived probes. Two areas of concern are the design and analysis of such experiments. Microarrays are rapidly producing enormous amounts of raw data. The bioinformatics solutions to problems associated with the analysis of data on this scale are a major current challenge. In addition, designing such experiments requires consideration of not only the genomic information required to answer a given problem but also consideration of the chemistry and physics of highly charged species near prepared surfaces.