Engineering DNA Origami Structures On Cell Surface for Detection of Cancer Biomarkers in Cellular Microenvironment

By: Melika Shahhosseini

Cancer cells exhibit specific gene mutations, such as mutations in the tumor suppressor gene BRCA1 that are observed in breast cancer. Circulating tumor DNA (ctDNA) are the mutated genes that are released by dead cancer cells into blood circulation, which presents a potential marker for early stage diagnosis. There are currently multiple methods to detect ctDNAs for early cancer diagnosis, normally by performing liquid biopsies. However, current detection methods have limitations such as demand for specialized equipment, low sensitivity and insufficient specificity. Furthermore, none of the available techniques provide in-situ detection, which may provide the additional benefit of elucidating mechanisms of cancer progression mediated by ctDNA. To address these limitations, we aim to exploit cells as sensing platforms by engineering their cell membranes to detect ctDNA in-situ with fluorescence based reporting. DNA origami is self-assembly of geometric complex nanostructures using DNA as building blocks. We recently reported a highly novel approach to engineer cell-membrane function by embedding DNA-origami nanodevices onto the cell surface via cholesterol-conjugated oligonucleotides as amphiphilic anchors [3]. We programmed DNA origami nanodevices to detect presence of 2 different DNA sequence (targets) on the cell surface by emitting fluorescence signal in two different channels. Preliminary results show that introduction of each DNA target at 1μM, increases fluorescence signal by 50%. Also, structures are able to simultaneously detect two target DNA sequences over a broad range of concentrations (1nM to 1μM). Preliminary results also suggest we can detect binding events on individual cells, and in some cases with sub-cellular resolution. Therefore, we expect that implementing DNA origami structures on cell membranes will enable us to profile the spatiotemporal distribution of ctDNA in cellular microenvironment. For future steps, we plan to incorporate multiple cancer-related aptamers into DNA structures to enable simultaneous detection of multiple cancer biomarkers. Specifically, we are interested in detection of combinations of different cancer related genes with other cancer biomarkers (e.g. platelet-derived growth factor and pH) in cellular microenvironment. This technique can be implemented as a highly sensitive liquid biopsy method for early detection of cancer.