Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor

• Published in: Scientific reports Vol. 9; no. 1; pp. 11056 - 10
• Main Authors: Chou, Wei-Cheng, Hu, Wen-Pin, Yang, Yuh-Shyong, Chan, Hardy Wai-Hong, Chen, Wen-Yih
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.07.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38/71; 639/925/352/1060; 639/925/930/12; 9/10; 96/10; Biosensing Techniques - methods; Deoxyribonucleic acid; DNA; DNA Probes - genetics; Genetic analysis; Genotyping Techniques - methods; Hepatitis C; Humanities and Social Sciences; multidisciplinary; Nanotechnology; Nanowires; Nanowires - chemistry; Nucleotide sequence; Polymorphism, Single Nucleotide; Precision medicine; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Sensitivity and Specificity; Silicon - chemistry; Single-nucleotide polymorphism; Transistors, Electronic
• DOI: 10.1038/s41598-019-47522-9
• ISSN: 2045-2322

Silicon nanowire (SiNW) field-effect transistors (FETs) is a powerful tool in genetic molecule analysis because of their high sensitivity, short detection time, and label-free detection. In nucleic acid detection, GC-rich nucleic acid sequences form self- and cross-dimers and stem-loop structures, which can easily obtain data containing signals from nonspecific DNA binding. The features of GC-rich nucleic acid sequences cause inaccuracies in nucleic acid detection and hinder the development of precision medicine. To improve the inaccurate detection results, we used phosphate-methylated (neutral) nucleotides to synthesize the neutralized chimeric DNA oligomer probe. The probe fragment originated from a primer for the detection of hepatitis C virus (HCV) genotype 3b, and single-mismatched and perfect-matched targets were designed for single nucleotide polymorphisms (SNP) detection on the SiNW FET device. Experimental results revealed that the HCV-3b chimeric neutralized DNA (nDNA) probe exhibited better performance for SNP discrimination in 10 mM bis-tris propane buffer at 25 °C than a regular DNA probe. The SNP discrimination of the nDNA probe could be further improved at 40 °C on the FET device. Consequently, the neutralized chimeric DNA probe could successfully distinguish SNP in the detection of GC-rich target sequences under optimal operating conditions on the SiNW FET device.