High sensitivity electrochemical DNA sensors for detection of somatic mutations in FFPE samples

TL;DR

This paper presents a new high-sensitivity, label-free electrochemical DNA sensor platform using crystalline carbon nanotube arrays for detecting somatic mutations in FFPE samples, achieving attomolar detection limits.

Contribution

The study introduces a novel electrochemical impedimetric DNA sensor based on CNT arrays fabricated by LB deposition for detecting mutations in FFPE samples, with enhanced sensitivity.

Findings

Detected KRAS mutations in FFPE tumor samples.

Achieved attomolar DNA detection sensitivity.

Successfully discriminated specific gene mutations.

Abstract

We offer new high-performance label-free electrochemical impedimetric DNA sensors of non-faradaic type. The DNA sensors based on a platform of crystalline carbon nanotube (CNT) arrays are fabricated by the Langmuir--Blodgett (LB) deposition technique. The CNT arrays are suspended on a nanoporous anodic alumina (aluminium oxide, AOA) support. Single-stranded (ss) 19- and 20-base oligonucleotides and double-stranded (ds) nucleotide sequences were used as probes for chosen molecular target -- human KRAS (Kirsten Rat Sarcoma viral oncogene homolog) gene. Genomic deoxyribonucleic acids (DNAs) were isolated from placenta of healthy donors and FFPE (formalin-fixed, paraffinembedded) samples of tumor tissue. Raman spectral analysis and electrochemical dielectric spectroscopy were used to sequence the target DNAs. The optical and electrochemical detection (variants of DNA sequencing) were based on a screening effect that grows after the DNA homoduplex formation. We demonstrated that such technologies are very sensitive and allow to detect attomolar DNA concentrations and less. As result, the KRAS exon 2, codon 12, c.35G$>$A mutation was successfully discriminated in human genomic DNA isolated from FFPE colorectal cancer tumor tissue samples.