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

Abstract

Simultaneously studying different biomarker types (DNA, RNA, proteins, etc.) could improve understanding and diagnosis of many complex diseases. However, biomarker detection involves several complex or expensive methodologies, requiring specialized laboratories and personnel. A multiplexed assay would greatly facilitate the use of 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. The resulting distinctly-sized fragments yield characteristic gel electrophoresis band patterns. This has enabled us to detect with high sensitivity and specificity DNA sequences including BRCA1 (limit of detection, LOD, ∼3 nM), RNA (miR-141, LOD ∼19 nM) and the steroids aldosterone and cortisol (LOD ∼200–250 nM). We show that our assay is multiplexable, and 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.