The nuclease hybridization assay, also called S1 nuclease cutting assay, is a nuclease protection assay-based hybridization ELISA. The assay is using S1 nuclease, which degrades single-stranded DNA and RNA into oligo- or mononucleotides, leaving intact double-stranded DNA and RNA.
In the nuclease hybridization assay, the oligonucleotide analyte is captured onto the solid support such as a 96-well plate via a fully complementary cutting probe. After enzymatic processing by S1 nuclease, the free cutting probe and the cutting probe hybridized to metabolites, i.e. shortmers of the analyte are degraded, allowing signal to be generated only from the full-length cutting probe-analyte duplex.
The assay is well tolerant to diverse chemistries, as exemplified by the development of a nuclease assay for morpholino oligonucleotides.
This assay set-up can lack robustness and is not suitable for validation following the FDA's guidelines for [https://www.fda.gov/files/drugs/published/Bioanalytical-Method-Validation-Guidance-for-Industry.pdf bioanalytical method validation].  This is demonstrated by an absence of published method that have been validated to the standards outlined by the FDA for bioanalytical methods.