In-stem molecular beacon targeted to a 50-region of tRNA inclusive of the D arm that detects mature tRNA with high sensitivity

Yuichi Miyoshi, Takashi Ohtsuki, Hiromu Kashida, Hiroyuki Asanuma, Kazunori Watanabe

Research output: Contribution to journalArticle

Abstract

Cellular functions are regulated by the up- and down-regulation and localization of RNA molecules. Therefore, many RNA detection methods have been developed to analyze RNA levels and localization. Molecular beacon (MB) is one of the major methods for quantitative RNA detection and analysis of RNA localization. Most oligonucleotide-based probes, including MB, are designed to target a long flexible region on the target RNA molecule, e.g., a single-stranded region. Recently, analyses of tRNA localization and levels became important, as it has been shown that environmental stresses and chemical reagents induce nuclear accumulation of tRNA and tRNA degradation in mammalian cells. However, tRNA is highly structured and does not harbor any long flexible regions. Hence, only a few methods are currently available for detecting tRNA. In the present study, we attempted to detect elongator tRNAMet (eMet) and initiator tRNAMet (iMet) by using an in-stem molecular beacon (ISMB), characterized by more effective quenching and significantly higher sensitivity than those of conventional MB. We found that ISMB1 targeted a 50- region that includes the D arm of tRNA and that it detected eMet and iMet transcripts as well as mature eMet with high sensitivity. Moreover, the analysis revealed that the formation of the ISMB/tRNA transcript complex required more time than the formation of an ISMB/unstructured short RNA complex. These results suggest that ISMB-based tRNA detection can be a useful tool for various biological and medical studies.

Original languageEnglish
Article numbere0211505
JournalPLoS One
Volume14
Issue number1
DOIs
Publication statusPublished - Jan 1 2019

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Transfer RNA
RNA
stems
RNA, Transfer, Met
Molecules
oligonucleotides
Oligonucleotide Probes
Ports and harbors
quantitative analysis
Oligonucleotides
Quenching
Up-Regulation
Down-Regulation
Cells
degradation
Degradation
methodology

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

In-stem molecular beacon targeted to a 50-region of tRNA inclusive of the D arm that detects mature tRNA with high sensitivity. / Miyoshi, Yuichi; Ohtsuki, Takashi; Kashida, Hiromu; Asanuma, Hiroyuki; Watanabe, Kazunori.

In: PLoS One, Vol. 14, No. 1, e0211505, 01.01.2019.

Research output: Contribution to journalArticle

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