Development of Magnetic Fluidic SELEX to Select HE4 Ovarian Cancer Biomarker Aptamers

Science Center, Bent Corridor

The detection of biomarkers is a powerful aid in the diagnosis and treatment of many diseases including cancer. Our work focuses on selecting high-affinity nucleic acid aptamers for the ovarian cancer biomarker HE4. This report describes our development and optimization of techniques to aid our previous selection process resulting in a combinatorial technique new to the Whelan lab called magnetic fluidic SELEX. As suggested by its name, magnetic fluidic SELEX makes use of magnetic Ni2+ beads equilibrated with HE4-6-His to fix and separate strongly binding potential aptamers from weakly binding potential aptamers as well as a fluidics platform to aid in washing. In addition, we improved single stranding and aptamer clean-up by optimizing asymmetric PCR and gel extraction. We used this new system for five rounds of SELEX, after which each of the five aptamer candidate pools were sequenced. Our preliminary examination of sequencing data reveals that the population of DNA has been substantially altered as rounds of SELEX progress. We expect to use capillary electrophoresis and fluorescence anisotropy to analyze the binding capabilities of top aptamer candidates.