title: Isolation and Identification of Post-Transcriptional Gene Silencing-Related Micro-RNAs by Functionalized Silicon Nanowire Field-effect Transistor.
abstract: 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.
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.|Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 106, Taiwan.
authors.forename: Kuan-I
authors.initials: KI
authors.lastname: Chen
authors.affiliation: Department of Life Science, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Chien-Yuan
authors.initials: CY
authors.lastname: Pan
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Keng-Hui
authors.initials: KH
authors.lastname: Li
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Ying-Chih
authors.initials: YC
authors.lastname: Huang
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Chia-Wei
authors.initials: CW
authors.lastname: Lu
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan.
authors.forename: Chuan-Yi
authors.initials: CY
authors.lastname: Tang
authors.affiliation: National Nano Device Laboratories, Hsinchu 300, Taiwan.
authors.forename: Ya-Wen
authors.initials: YW
authors.lastname: Su
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Ling-Wei
authors.initials: LW
authors.lastname: Tseng
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.|Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 106, Taiwan.
authors.forename: Kun-Chang
authors.initials: KC
authors.lastname: Tseng
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Chi-Yun
authors.initials: CY
authors.lastname: Lin
authors.affiliation: Institute of Physics, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Chii-Dong
authors.initials: CD
authors.lastname: Chen
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan.|Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Shih-Shun
authors.initials: SS
authors.lastname: Lin
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.|Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 106, Taiwan.
authors.forename: Yit-Tsong
authors.initials: YT
authors.lastname: Chen
mesh_terms: D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods; D020868:Gene Silencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D036103:Nanotechnology / Q000295:instrumentation* / Q000379:methods*; D053770:Nanowires; D009690:Nucleic Acid Conformation; D034622:RNA Interference; D012323:RNA Processing, Post-Transcriptional; D012825:Silicon; D014173:Transistors, Electronic
chemical_list: D035683:MicroRNAs; D012825:Silicon