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.
Highlights
The silicon nanowire (NW) field-effect transistor (FET), as a biosensor, promises ultra-high sensitivity in the detection of a variety of proteins[1], nucleic acids[2,3,4], and metal cations[5]
Peptide nucleic acid (PNA), locked nucleic acid (LNA), phosphoramidate morpholino (MORF), and hexitol nucleic acid oligomers have been employed in therapeutic applications; these DNA analogs exhibit better biostability in body than regular nucleic acids without compromising the specific ability to the complementary target nucleic acids[7]
The target DNA samples, including cH1 and ncH1, were all prepared at 1 pM in 1 mM bis-tris propane (BTP)
Summary
The silicon nanowire (NW) field-effect transistor (FET), as a biosensor, promises ultra-high sensitivity in the detection of a variety of proteins[1], nucleic acids[2,3,4], and metal cations[5]. The neutrally charged PNA can significantly improve DNA-binding efficiency, and the PNA used as a capture probe/receptor in the FET-based biosensor can achieve ultrasensitive label-free detection of nucleic acid fragments[7,8]. Higher degree of probe immobilization, improved hybridization efficiency, and the prevention of charge interference from the probe are the virtues of using nDNA oligomers in the FET measurement for the detection of oligonucleotides[4] Other uncharged analogs, such as MORF oligomers and methylphosphonate oligonucleotides, are synthesized and mainly applied in therapeutic developments[10,11] and diagnostics[12]. We expected that the partially neutralized chimeric DNA probes could further improve the performance of the FET sensors in the measurement of target DNA to provide high-sensitive and high-accuracy detection results
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