Real-time Polymerase Chain Reaction (PCR) amplification is generally regarded as the most sensitive and specific means of detecting potential bio warfare pathogens. Results can usually be obtained in about an hour, including a separate sample preparation step to manually extract DNA signatures prior to PCR analysis. Well-characterized COTS DNA extraction kits are available for rapid extraction (20 to 30 minutes) of target DNA from a variety of complex liquid and solid matrices including food, water, and tissue. Samples are prepared by the end user and the instrument performs PCR amplification of the target sequences. Thermal cycling produces additional copies of target sequences, and the fluorescent levels in the reaction change as additional copies are produced. During thermal cycling, the instrument detects copies of the target sequences by measuring changes in fluorescence.

A major disadvantage of nucleic acid-based detection devices is their inability to directly detect non-nucleic acid targets such as toxins. However, toxins may be indirectly detected via the presence of residual DNA fragments of the organism used to produce the toxin. Residual DNA fragments from the organism used to produce a toxin are typically present at low levels even in the purest of toxin preparations, and fragments are most likely present in higher concentrations in crude preparations.