Synergetic improvements of sensitivity and specificity of nanowire field effect transistor gene chip by designing neutralized DNA as probe

Abstract

Neutral DNA analogs as probes for the detection of target oligomers on the biosensors based on the field-effect transistor (FET) configuration feature advantages in the enhancement of sensitivity and signal-to-noise ratio. Herein, we used phosphate-methylated nucleotides to synthesize two partially neutralized chimeric DNA products and a fully neutralized DNA sequence and adopted a regular DNA oligomer as probes on the polycrystalline silicon nanowire (NW) FET devices. The sequences of two neutralized chimeric DNAs close to the 5′ end were alternately modified with the phosphate-methylated nucleotides, and all probes were immobilized via their 5′ end on the NW surface. The non-specific-to-specific binding ratio indicated that the two 5′-end partially neutralized chimeric DNAs featured better performance than the regular and fully neutralized DNA oligomers. The partially neutralized probe design reduces the ionic strength needed for hybridization and increases the Debye length of detection, thus promoting the detection sensitivity of FET and achieving the limit of detection of 0.1 fM. By using an appropriate probe design, applying DNA oligomers with embedded phosphate-methylated nucleotides in the FET biosensors is a promising way for gene detection with high sensitivity and specificity.

Combination of Aptamer Amplifier and Antigen-Binding Fragment Probe as a Novel Strategy to Improve Detection Limit of Silicon Nanowire Field-Effect Transistor Immunosensors

“…The electrical response of biosensing performance by SiNWFET immunosensors, which were fabricated from n-type devices provided by Episil Technologies Inc. (Hsinchu, Taiwan) and have been used in our recent publications [ 17 , 18 , 31 , 32 , 33 ], were collected by Keithley 2636 Dual-Channel System Source Meter Instrument and a probe station with a chamber (Everbeing).…”

Biosensing based on field-effect transistors (FET): Recent progress and challenges

“…Between the currently developed FET-based genosensors that are presented in Table 5 , the device fabricated by Hu and coworkers showed an extraordinary performance. They functionalized the surface of polycrystalline silicon nanowire FET devices with DNA probes and attained a LOD of 0.1 fM [ 151 ]. In another successful work conducted by Hwang et al, FETs with a monolayer of graphene channel were utilized for the detection of DNA.…”

“… Application Target RE Linker Surface Sensor Readout LOD Sample Ref. Optimize the ionic strength and the debye length of the detection Target oligomers DNA oligomers APTES GA Poly-Si NW FET Off-chip 0.1 fM Buffer solution (BTP) [ 151 ] DNA detection DNA PNA APTES GA PASE ETA SiO 2 /Ti/Au/PMMA/SLG/copper/CVD-grown SLG G-FET Off-chip 10 fM Buffer solution (PBS) [ 153 ] Nucleic acid analysis Target DNA Probe DNA APTES EDC/NHS SiO 2 /Si 3 N 4 /SWNT CMOS-compatible SiNW-FET Off-chip 1 fM Buffer solution (PBS) [ 154 ] DNA hybridization sensing Target DNA Probe DNA APTES GA SiO 2 /Poly SiNW CMOS-compatible poly-Si NW FET Off-chip 1 fM Buffer solution (PBS) [ 155 ] DNA detection Target DNA Probe DNA PASE ETA PS/Graphene/PMMA/Silicone rubber FET Off-chip 20 aM Serum [ 152 ] ETA: ethanolamine, SLG: single-layer graphene, PNA: peptide nucleic acid, PASE: 1-Pyrenebutanoic acid succinimidyl ester, PS: polystyrene

Fig.10 Illustration of the flat and crumpled graphene FET genosensor. b fabrication of FETs and investigational flow of the procedure [ 152 ...

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Field-Effect Transistor Biosensors for Biomedical Applications: Recent Advances and Future Prospects

“…The novelty of this technique comes from DNA helpers, which can trigger target recycling and hybridization chain reaction, lead to signal enhancement of biorecognition events and therefore rocket sensitivity up to 20,000 × (LOD ≈ 5 fM for 21-mer detection) compared to previous publications [95]. Another exclusive design of nucleotide-probe comes from neutralized DNA (nDNA; developed from a research activated in 2013 [27]), in which two partially neutralized DNA exhibited better sensitivity and selectivity than the regular and fully neutralized DNA in hybridization (reached LOD of 0.1 fM) [28]. nDNA can also greatly discriminate between perfect- and mismatched sequences of GC-rich single nucleotide polymorphisms (GC content: 75%) although the hybridization should be carried out in low ionic strength environment (10 mM Bis-Tris propane) in order to maximize the discrimination effect [62].…”

“…However, in spite of continuous advancement in large-scale assembly techniques (fluid flow directed assembly [15], bubble-blown assembly [16], contact assembly [17], electric-field-assisted assembly [18], Langmuir-Blodgett assembly [19], field-assisted electrospinning [20], the “place then grow” method [21] and superlattice nanowire pattern transfer [22]) with a well-controlled dimension, orientation and density of synthesized nanowires [23], high device-to-device variation and low carrier mobility are primary issues crucially overcome on the way to commercialize SiNWFETs [24]. Since SiNWFET-based sensors have been successfully employed to detect a variety of biological and chemical molecules (proteins [9,10,11,12,13,25], nucleic acids [14,25,26,27,28], viruses [29,30] and different targeted substances [9,31,32,33,34]), there have been plentiful strategies to improve their sensing capability by operating detection in subthreshold regime [35], using frequency domain measurement [36], optimizing surface modification with electrical field alignment [37], integrating with nanopore morphology [38] or electrokinetic devices [39], and fabricating branched nanowires [40] for clinical diagnosis, the ultimate goal of profuse biomedical applications [41]. CNTs, whereas, possess superior physical and chemical properties for biosensor applications such as: High mechanical strength, surface area and aspect ratio, excellent chemical and thermal stability [42]; outstanding conductivity for nanoscale transducers [43,44,45] and ideal semiconducting behavior as nanoscale FETs [46]; especially advantageous to immobilize bio-probes (antibodies, enzymes, oligonucleotides, etc.)…”