Detection of Unlabeled Oligonucleotides in FFPE Tissue Sections Using Automated miRNAscope Assays

Investigations into the pharmacokinetic distribution of unlabelled drugs in tissue can often be challenging, especially when the drug moiety is an oligonucleotide. Detecting the cellular distribution of specific nucleotide sequences of short (17-25 nucleotide) single- or double-stranded unconjugated oligonucleotides in formalin-fixed paraffin embedded tissue sections is required to understand, where the biodistribution of the drug is at the whole organ and tissue level, down to subcellular resolution. To address this, we present here new chromogenic and fluorescent commercial in situ hybridization-based assays that allow us to specifically and sensitively detect unconjugated oligonucleotides down to subcellular resolution, irrespective of backbone chemistry and modifications. These assays can also be run as ISH-IHC or ISH-IF co-detection protocols to determine cell lineages and represent a powerful and versatile tool in the drug discovery repertoire.