A flap endonuclease 1-assisted universal viral nucleic acid sensing system using surface-enhanced Raman scattering

Joowon Park, Jinyoung Kim, Chaewon Park, Jong Woo Lim, Minjoo Yeom, Daesub Song, Eunjung Kim, Seungjoo Haam

Research output: Contribution to journalArticlepeer-review

Abstract

The continued uncertainty of emerging infectious viral diseases has led to an extraordinary urgency to develop advanced molecular diagnostic tests that are faster, more reliable, simpler to use, and readily available than traditional methods. This study presents a system that can accurately and rapidly trace viral nucleic acids by employing flap endonuclease 1 (FEN1)-assisted specific DNA cleavage reactions and surface-enhanced Raman scattering (SERS)-based analysis. The designed Raman tag-labeled 5′- and 3′-flap provider DNA yielded structurally defined DNA substrates on magnetic nanoparticle surfaces when a target was present. The FEN1 enzyme subsequently processes the substrates formed via an invasive cleavage reaction, producing 5′-flap DNA products. Magnetic separation allows efficient purification of flap products from reaction mixtures. The isolated solution was directly applied onto high aspect-ratio plasmonic silver nanopillars serving as SERS-active substrates to induce amplified SERS signals. We verified the developed SERS-based sensing system using a synthetic target complementary to an avian influenza A (H9N2) virus gene and examined the detection performance of the system using complementary DNA (cDNA) derived from H9N2 viral RNA. As a result, we could detect a synthetic target with a detection limit of 41.1 fM with a single base-pair discrimination ability and achieved multiplexed detection capability for two targets. Using cDNA samples from H9N2 viruses, we observed a high concordance of R2 = 0.917 between the data obtained from SERS and the quantitative polymerase chain reaction. We anticipate that this enzyme-assisted SERS sensor may provide insights into the development of high-performance molecular diagnostic tools that can respond rapidly to viral pathogens.

Original languageEnglish
Pages (from-to)5028-5037
Number of pages10
JournalAnalyst
Volume147
Issue number22
DOIs
Publication statusPublished - 2022 Oct 3

Bibliographical note

Funding Information:
E. Kim acknowledges support from the National Research Foundation (NRF) of Korea grant funded by the Ministry of Science and ICT (MSIT) of Korea (NRF-2020R1F1A1066247, NRF-2022R1C1C1005390) and the Industrial Strategic Technology Development Program (20009121) funded by the Ministry of Trade, Industry & Energy (MOTIE) of Korea. S. Haam acknowledges support from Korea Environment Industry & Technology Institute (KEITI) through Technology Development Project for Biological Hazards Management in Indoor Air Project, funded by Korea Ministry of Environment (MOE) (RE202101004) and the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science & ICT (NRF-2018M3A9E2022819).

Publisher Copyright:
© 2022 The Royal Society of Chemistry.

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biochemistry
  • Environmental Chemistry
  • Spectroscopy
  • Electrochemistry

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