Microarrays of oligonucleotides which represent the complete set of complements to a target RNA are readily made by a simple automated method. These ‘scanning’ arrays can be used for basic studies of the hybridization reaction, which is the basis of all microarray techniques. We have studied the influence of secondary and tertiary structure in the RNA and found that it is mainly this which determines the extent of hybridization, rather than base composition or sequence. We also find that the folded structure is formed during transcription process, which indicates that computer-based prediction of RNA folding by finding the structure with the minimum global free energy is over-simple.

In addition to these fundamental studies, ‘scanning’ arrays are useful for the selection of antisense reagents, which are increasingly used for gene ablation to discover the functions of genes emerging from sequencing programmes. Antisense methods are very simple, but only a fraction of potential sequences provide effective targets. These can be found by hybridization of the transcript to a complete set of complements represented on the array.