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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| Format: | Article |
| Language: | English |
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Nature Portfolio
2019-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-019-47522-9 |
| _version_ | 1818994342809829376 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-20T20:56:26Z |
| format | Article |
| id | doaj.art-289625770b6046129601345e4434cd0e |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-20T20:56:26Z |
| publishDate | 2019-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-289625770b6046129601345e4434cd0e2022-12-21T19:26:49ZengNature PortfolioScientific Reports2045-23222019-07-019111010.1038/s41598-019-47522-9Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistorWei-Cheng Chou0Wen-Pin Hu1Yuh-Shyong Yang2Hardy Wai-Hong Chan3Wen-Yih Chen4Department of Chemical and Materials Engineering, National Central UniversityDepartment of Bioinformatics and Medical Engineering, Asia UniversityInstitute of Biological Science and Technology, National Chiao Tung UniversityHelios Bioelectronics, Inc. 3F.Department of Chemical and Materials Engineering, National Central UniversityAbstract 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.https://doi.org/10.1038/s41598-019-47522-9 |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-019-47522-9 |
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