The technique can identify one or more RNA molecules of known sequence even at low total concentration.
When the reaction runs to completion, susceptible RNA regions are degraded to very short oligomers or to individual nucleotides; the surviving RNA fragments are those that were complementary to the added antisense strand and thus contained the sequence of interest.
The probes are prepared by cloning part of the gene of interest in a vector under the control of any of the following promoters, SP6, T7 or T3.
These promoters are recognized by DNA dependent RNA polymerases originally characterized from bacteriophages.
Nuclease protection assays are used to map introns and 5' and 3' ends of transcribed gene regions.