Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

Abstract

We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics.

Fig. 1.

Fluorescence microscopy images of the NTNFET devices with distance between electrodes of 10 μm after DNA incubations for 1 h followed by removing unbound DNA oligomers. Images after incubation with Cy5-labeled (A) and unlabeled (B) 12-mer oligonucleotide capture probes (5′-CCT AAT AAC AAT-3′). (C) The device with the unlabeled DNA capture probes after incubation with FITC-labeled complementary DNA target (5′ Fitc-ATT GTT ATT AGG-3′). Another set of experiments included dA₁₂ as a capture DNA probe. (D) Image after incubation with Cy5-labeled A₁₂ captures. (E) The device after incubation with the FITC-labeled DNA targets, which have homology with only six bases in dA₁₂ captures. (Image before the target incubation is not shown.) (F) The graph associated with C and E. The fluorescent signals were measured as a difference between carbon nanotube device area and bare silicon wafer after a 20-sec integration.

Fig. 2.

Electronic measurements such as source-drain conductance (G) as function of gate voltage (V_g), and schematic drawings of the NTNFET devices used for DNA assays. (A) Before (bare NT) and after incubation with 12-mer oligonucleotide capture probes (5′-CCT AAT AAC AAT-3′), as well as after incubation with the complementary FITC-labeled DNA targets. (B) Before and after incubation with dA₁₂ captures as well as after incubation with the DNA targets.

Fig. 3.

Electronic detection of the presence of SNP in synthetic HFE amplicons. (A) G–V_g curves after incubation with allele-specific wild-type capture probe and after challenging the device with wild-type synthetic HFE target (50 nM). (B) G–V_g curves in the experiment with mutant capture probe. (C) Graph with electronic (1 – G/G₀) and fluorescent responses in SNP detection assays. For electronic response, average of normalized signals for three NTNFET devices were calculated. Error bars are equal to one standard deviation. (D) Graph with electronic (1 – G/G₀) responses in SNP detection assay (n = 4, P = 0.002) using 100 pM wt target in the presence of 5 μg/ml heat-denatured salmon DNA. no block, PB buffer; TX100 block, 0.01% Triton X-100 in PB buffer for 15 min at room temperature.

Fig. 4.

Source-drain conductance (G) as function of gate voltage (V_g) of three NTNFET devices used for titration experiments with unlabeled oligonucleotides. (A) G–V_g curves before (bare) and after incubation with capture probe (ss-DNA) (5 μM in 200 mM PB, pH 7.2) as well as after incubations with target (c-DNA) (1, 10, 50, 100, and 200 nM in 200 mM PB). (B) As in A, except that incubations were conducted with target (c-DNA) (1, 10, 50, 100, and 200 nM in 10 mM PB/20 mM MgCl₂). (C) As in A but incubations with target (c-DNA) (1, 10, and 50 pM, and 1 nM in 10 mM PB/20 mM MgCl₂). (D) Plot of normalized conductance (G/G₀) of the three NTNFET devices as function of target DNA concentrations.

Fig. 5.

Scanning electron microscopy image of the random network NTNFET device. The distance between source (S) and drain (D) interdigitated metal electrodes is 10 μm.