Abstract: The present invention relates to compositions, apparatus and methods useful for concurrently performing singular, multiple, high throughput, biological or chemical assays, using nuclease protection molecules which specifically bind to a target of interest. The nuclease protection molecules are capable of detecting targets in complex biological samples, including, preserved, fixed, dried, and/or cross-linked specimen. The reagents and methods of the instant invention provide an effective means for analyzing a target of interest from a complex biological sample without solubilizing or disrupting the sample. Utilization of such methods in clinical and/or diagnostic applications is also described.