Isolation and Identification of Post-Transcriptional Gene Silencing-Related Micro-RNAs by Functionalized Silicon Nanowire Field-effect Transistor

• Published in: Scientific reports Vol. 5; no. 1; p. 17375
• Main Authors: Chen, Kuan-I, Pan, Chien-Yuan, Li, Keng-Hui, Huang, Ying-Chih, Lu, Chia-Wei, Tang, Chuan-Yi, Su, Ya-Wen, Tseng, Ling-Wei, Tseng, Kun-Chang, Lin, Chi-Yun, Chen, Chii-Dong, Lin, Shih-Shun, Chen, Yit-Tsong
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.11.2015; Nature Publishing Group
• Subjects: 38/90; 631/61/350/59; 639/925/350/59; 9/10; Gene Expression Profiling - instrumentation; Gene Expression Profiling - methods; Gene Silencing; Humanities and Social Sciences; MicroRNAs - chemistry; MicroRNAs - genetics; multidisciplinary; Nanotechnology - instrumentation; Nanotechnology - methods; Nanowires; Nucleic Acid Conformation; RNA Interference; RNA Processing, Post-Transcriptional; Science; Silicon; Transistors, Electronic
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep17375

Many transcribed RNAs are non-coding RNAs, including microRNAs (miRNAs), which bind to complementary sequences on messenger RNAs to regulate the translation efficacy. Therefore, identifying the miRNAs expressed in cells/organisms aids in understanding genetic control in cells/organisms. In this report, we determined the binding of oligonucleotides to a receptor-modified silicon nanowire field-effect transistor (SiNW-FET) by monitoring the changes in conductance of the SiNW-FET. We first modified a SiNW-FET with a DNA probe to directly and selectively detect the complementary miRNA in cell lysates. This SiNW-FET device has 7-fold higher sensitivity than reverse transcription-quantitative polymerase chain reaction in detecting the corresponding miRNA. Next, we anchored viral p19 proteins, which bind the double-strand small RNAs (ds-sRNAs), on the SiNW-FET. By perfusing the device with synthesized ds-sRNAs of different pairing statuses, the dissociation constants revealed that the nucleotides at the 3′-overhangs and pairings at the terminus are important for the interactions. After perfusing the total RNA mixture extracted from Nicotiana benthamiana across the device, this device could enrich the ds-sRNAs for sequence analysis. Finally, this bionanoelectronic SiNW-FET, which is able to isolate and identify the interacting protein-RNA, adds an additional tool in genomic technology for the future study of direct biomolecular interactions.