Multiplexed Label-Free Biomarker Detection by Targeted Disassembly of Variable-Length DNA Payload Chains

Simultaneously studying different biomarker types (DNA, RNA, proteins, etc.) has the potential to significantly improve understanding and diagnosis of many complex diseases. However, biomarker detection involves several complex or expensive methodologies, often requiring specialized laboratories and personnel. A multiplexed assay would greatly facilitate the process of accessing biomarker data. Here, we present a multiplexed biomarker detection technique using variable-length DNA payload chains, which are systematically disassembled in the presence of specific biomarkers, releasing distinctly-sized fragments that yield characteristic gel electrophoresis band patterns. This strategy has enabled us to detect with high sensitivity and specificity DNA sequences including BRCA1, RNA (miR-141) and the steroids aldosterone and cortisol. We show that our assay is multiplexable, enabling simultaneous biomarker detection. Furthermore, we show that our method suffers limited sensitivity loss in fetal bovine serum and can be applied using capillary electrophoresis, which may be more amenable to automation and integration in healthcare settings.