Electronic DNA detection and diagnostics

Abstract

The Nanopill project is an ambitious undertaking with the objective to develop an early-warning cancer diagnostic pill that is ingested by the patient. The Nanopill collects intestinal fluid as the pill travels down the intestinal tract, and tests for the presence of a free floating hyper-methylated DNA (hm-DNA) with a gene sequence specific for colorectal cancer. Since the development of the entire Nanopill system is beyond the scope of a single doctoral thesis, this thesis focused on the development and realization of an automated microscale bioassay for the capture and enrichment of the hm-DNA colorectal cancer marker and the subsequent detection of the specific DNA sequence using all-electronic silicon nanowire (Si-NW) biosensors without the use of amplification. Free-floating hm-DNA is present in very low concentrations in biological samples, such as stool, sputum, urine, blood, and gastrointestinal fluid. A capture and pre-concentraion of hm-DNA would be used, prior to detection on Si-NWs. The pre-concentration system has been designed and implemented using a pillar-based glass-silicon microfluidic chip for the solid-phase extraction of hm-DNA with methyl binding domain (MBD) protein that specifically captures double-stranded hm-DNA in the CpG island hyper-methylation context. The MBD extraction microchip is designed for the capture and elution of hm-DNA with quantities less than 1 ng ml-1 and was able to demonstrate 28× concentration factor of the input concentration. The DNA detection assay is based on Si-NW biosensors that are integrated into a microfluidic auto-sampler system with automated sample delivery to the sensors eliminating erroneous sensor signals during sample switching. The Si-NWs detect the surface potential change due to surface charge density changes on the surface of the gate-oxide. This principle has been used to detect the negative electronic charge on the DNA backbone using specific base pairing to complementary uncharged peptide nucleic acid (PNA) probes attached to Si-NW gate-oxide surfaces. The research goals for the Nanopill assay have been demonstrated in principle and various solutions to identified problems offered. The microfluidic solid phase hm-DNA enrichment system and the electronic detection of DNA are functional and promising for further application in a single platform two-step assay.