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

Abstract 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 stru...

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Autores principales:	Wei-Cheng Chou, Wen-Pin Hu, Yuh-Shyong Yang, Hardy Wai-Hong Chan, Wen-Yih Chen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/289625770b6046129601345e4434cd0e
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spelling	oai:doaj.org-article:289625770b6046129601345e4434cd0e2021-12-02T15:07:52ZNeutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor10.1038/s41598-019-47522-92045-2322https://doaj.org/article/289625770b6046129601345e4434cd0e2019-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-47522-9https://doaj.org/toc/2045-2322Abstract 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.Wei-Cheng ChouWen-Pin HuYuh-Shyong YangHardy Wai-Hong ChanWen-Yih ChenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-10 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wei-Cheng Chou Wen-Pin Hu Yuh-Shyong Yang Hardy Wai-Hong Chan Wen-Yih Chen Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor
description	Abstract 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.
format	article
author	Wei-Cheng Chou Wen-Pin Hu Yuh-Shyong Yang Hardy Wai-Hong Chan Wen-Yih Chen
author_facet	Wei-Cheng Chou Wen-Pin Hu Yuh-Shyong Yang Hardy Wai-Hong Chan Wen-Yih Chen
author_sort	Wei-Cheng Chou
title	Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor
title_short	Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor
title_full	Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor
title_fullStr	Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor
title_full_unstemmed	Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor
title_sort	neutralized chimeric dna probe for the improvement of gc-rich rna detection specificity on the nanowire field-effect transistor
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/289625770b6046129601345e4434cd0e
work_keys_str_mv	AT weichengchou neutralizedchimericdnaprobefortheimprovementofgcrichrnadetectionspecificityonthenanowirefieldeffecttransistor AT wenpinhu neutralizedchimericdnaprobefortheimprovementofgcrichrnadetectionspecificityonthenanowirefieldeffecttransistor AT yuhshyongyang neutralizedchimericdnaprobefortheimprovementofgcrichrnadetectionspecificityonthenanowirefieldeffecttransistor AT hardywaihongchan neutralizedchimericdnaprobefortheimprovementofgcrichrnadetectionspecificityonthenanowirefieldeffecttransistor AT wenyihchen neutralizedchimericdnaprobefortheimprovementofgcrichrnadetectionspecificityonthenanowirefieldeffecttransistor
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Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor

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