The advent of the DNA microarray technology makes it possible to build an array of hundreds of thousands of DNA sequences, or probes, in a very small area, typically a few square centimeters on the surface of a microscopic slide. See, e.g., PCT patent publication Nos. WO 99/42813, 92/10092 and 90/15070, and U.S. Pat. No. 5,143,854, each of which is hereby incorporated by reference in its entirety. A DNA microarray-based assay usually involves hybridizing a DNA or RNA sample to a microarray and scanning the microarray to detect hybridization. The probes in the microarray are organized into areas of similar probes, these areas being referred to as features. By hybridizing experimental DNA or RNA to the probes on the microarray, and detecting in which features the experimental DNA or RNA has hybridized, it becomes possible to obtain much information about the experimental DNA or RNA in a single step relatively simple process. Using this ability, DNA microarray technology has been applied to areas such as gene expression and discovery, mutation detection, allelic and evolutionary sequence comparison, genome mapping, and more.
A state of the art DNA microarray can accommodate hundreds of thousands of features, each containing unique probes. In fact this capacity can exceed the needs of many common useful experiment, many of which involve hybridization assays involving far less probes than a microarray's full capacity. Therefore, some microarrays are constructed in which a set of features are repeated multiple times over the area of the microarray, with each set of features ultimately being exposed to a separate experimental sample, to conduct multiple data collection experiments in parallel. This concept can be thought of as an array of arrays. To do this, it is desirable to make DNA microarrays that can be simultaneously used for multiple samples. To make this work, there must be measures taken to prevent cross-contamination between samples intended for differing areas of the microarray. Currently, the microarrays built for this purpose (e.g., U.S. Pat. No. 5,874,219) use physical wells to separate probe sets for different samples and well walls have to align with corresponding probe sets so that each well contains the correct probes. However, alignment of well walls with corresponding probe sets is not always easy to achieve and a misalignment can lead to inaccurate result.