A Quencher-Free Linear Probe from Serinol Nucleic Acid with a Fluorescent Uracil Analogue

Chembiochem. 2020 Jan 15;21(1-2):120-128. doi: 10.1002/cbic.201900498. Epub 2019 Nov 21.

Abstract

With the goal of developing a quencher-free probe composed of an artificial nucleic acid, the fluorescent nucleobase analogue 5-(perylenylethynyl)uracil (Pe U), which was incorporated into totally artificial serinol nucleic acid (SNA) as a substitute for thymine, has been synthesized. In the context of a 12-mer duplex with RNA, these fluorophores reduce duplex stability slightly compared with that of an SNA without Pe U modification; thus suggesting that structural distortion is not induced by the modification. If two Pe Us were incorporated at separate positions in an SNA, the fluorescent emission at λ≈490 nm was clearly enhanced upon hybridization with complementary RNA. A quencher-free SNA linear probe containing three Pe Us, each separated by six nucleobases, has been designed. Detection of target RNA with high sensitivity and discrimination of a single-base mismatch has also been demonstrated.

Keywords: artificial nucleobases; artificial oligonucleotides; fluorescent probes; nucleic acids; perylenes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Fluorescence
  • Fluorescent Dyes / chemical synthesis
  • Fluorescent Dyes / chemistry*
  • Molecular Structure
  • Nucleic Acids / chemistry*
  • Propanolamines / chemistry*
  • Propylene Glycols / chemistry*
  • RNA / analysis*
  • Uracil / analogs & derivatives
  • Uracil / chemistry*

Substances

  • Fluorescent Dyes
  • Nucleic Acids
  • Propanolamines
  • Propylene Glycols
  • Uracil
  • RNA
  • serinol