Fluorophore–PNA–Quencher/Quencher–DNA probe for miRNA detection

Kentaro Tabara, Kazunori Watanabe, Hajime Shigeto, Shohei Yamamura, Takamasa Kishi, Mizuki Kitamatsu, Takashi Ohtsuki

Research output: Contribution to journalArticlepeer-review

Abstract

Micro RNAs (miRNAs) are involved in a variety of biological functions and are attracting attention as diagnostic and prognostic markers for various diseases. Highly sensitive RNA detection methods are required to determine miRNA expression levels and intracellular localization. In this study, we designed new double-stranded peptide nucleic acid (PNA)/DNA probes consisting of a fluorophore–PNA–quencher (fPq) and a quencher–DNA (qD) for miR-221 detection. We optimized the fPq structure, PNA–DNA hybrid length, and hybrid position. The resultant fPq-2/qD-6b probe was a 6-bp hybrid probe with a 10-base fPq and a 6-base qD. The signal-to-background ratios of the probes showed that fPq-2/qD-6b had a higher target sensitivity than fPq (PNA beacon)-type and fP/qD-type probes. The results of the detection limit and target specificity indicate that the fPq/qD probe is promising for RNA detection in both cells and cell extracts as well as for miRNA diagnosis.

Original languageEnglish
Article number128359
JournalBioorganic and Medicinal Chemistry Letters
Volume51
DOIs
Publication statusPublished - Nov 1 2021

Keywords

  • Micro RNA
  • PNA/DNA hybrid probe
  • Peptide nucleic acid
  • RNA detection

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry

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