Nanopore Activity Assays for Detection of Biomarker Protease Activity: Design and Testing of Substrates for Both Nanopore Sequencing and PCR-Based Detection Methods

The work performed in this project has demonstrated the ability to construct proteolytic enzyme substrates that are PCR and sequencing-readable reporter molecules. Specifically, the goal was to detect those reporter molecules via PCR and Oxford Nanopore Technologies MinION sequencing methods following exposure to the biomarker protease thrombin. The assay development focused on binding the constructed peptide-oligonucleotide chimera to immobilized streptavidin. The action of thrombin on the peptide portion of the molecule released the oligonucleotide for detection. Detection of protease activity was demonstrated in a concentration-dependent manner using MALDI-MS, RT-PCR and DNA sequencing. Additional steps to remove background release of reporter molecules during the assay was used to improve the difference in detected oligonucleotide reporter following protease activity. Additional steps in assay development will be to (1) test the assay in an appropriate matrix, (2) investigate detection using additional DNA sequencing platforms and (3) demonstrate multiplexed detection of multiple protease markers in a single reaction.. Authors: Wunschel, David S. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000156938514); Mobberley, Jennifer M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000158658145); Mo, Kai-For [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)]; Turner, Matthew W. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)]; Winans, Natalie M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)]. DOE Contract: AC05-76RL01830. Subjects: 59 BASIC BIOLOGICAL SCIENCES