Assay for nucleic acid detection employing nuclease protection fragments

The present invention relates to methods useful for concurrently performing assays for detecting nucleic acids and employing nuclease protection fragments. The assays may be using repeated arrays of probes. A surface, which comprises a plurality of test regions, at least two of which, and in a preferred embodiment, at least twenty of which, are substantially identical, wherein each of the test regions comprises an array of generic anchor molecules may be used. The anchors are associated with bifunctional linker molecules, each containing a portion which is specific for at least one of the anchors and a portion which is a probe specific for a target of interest. The resulting array of probes is used to analyze the presence or test the activity of one or more target molecules which specifically interact with the probes. A sample to be tested is subjected to a nuclease protection procedure before it is contacted with a combination of the invention.