An interference-based covalent organic framework biosensor for the detection of specific circulating tumor DNA in plasma

The accurate detection of circulating tumor DNA (ctDNA) in patients’ biological fluids can facilitate cancer diagnosis and prognosis. This study reports the development of a differential pulse voltammetric (DPV) biosensor for the detection of ctDNA coding for the key T790M lung cancer mutation of the epidermal growth factor receptor (EGFR). The biosensor was built with a working electrode (WE) made of optimized electroconductive particles comprising covalent organic frameworks (COF) displaying Au nanoparticles (Au NPs) modified with polyethyleneimine (COF@Au-PEI). Au NPs accelerated electron transfer while COFs and PEI maximized the architecture of the WE to improve electrochemical reactions and molecular probe binding. Next, hairpin DNA probes (haiDNA) specific to the EGFR T790M ctDNA analyte were bonded to COF@Au-PEI. Lastly, Au@Pt nanohybrids were attached to the WE to enhance its electrochemical performance. In this system, the long polynucleotide EGFR T790M ctDNA analyte interferes with electrochemical reactions upon binding to the haiDNA probes, resulting in a proportional decrease of the DPV signal. The device detected EGFR T790M ctDNA in blood plasma and exhibited good sensitivity, accuracy, stability, and reproducibility. The sensor was also highly selective with no DPV signal for the EGFR wildtype allele harboring a difference of only one base pair.