Optimal DNA structure of reverse-hairpin beacons for label-free and positive surface enhanced Raman scattering assays

Jisun Ki; Jinyoung Kim; Seeungmin Han; Eunji Jang; Taeksu Lee; Jung Sub Wi; Tae Geol Lee; Woonsung Na; Daesub Song; Seungjoo Haam

doi:10.1364/OME.7.002352

Optimal DNA structure of reverse-hairpin beacons for label-free and positive surface enhanced Raman scattering assays

Jisun Ki, Jinyoung Kim, Seeungmin Han, Eunji Jang, Taeksu Lee, Jung Sub Wi, Tae Geol Lee, Woonsung Na, Daesub Song, Seungjoo Haam

Department of Chemical and Biomolecular Engineering

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

We developed a label-free and positive-readout surface enhanced Raman scattering (SERS) assay using reverse-hairpin molecular beacons (RHBs) for the detection of RNA genetic markers associated with a high pathogenicity influenza (HPAI) virus. The structure of RHBs flexibly changed from a linear configuration (open state) to hairpin (closed state) upon targeting, such that the Raman label was closed on the SERS substrate and induced an increase of SERS intensity (OFF-to-ON). By improving sequence-specific RNA/DNA hybridization efficiency, we adjusted the stem-loop ratio of RHB, which was efficient at values of less than 1. The optimized RHBs exhibited dramatic changes in signal based on a fluorescence system in which the target was present. We demonstrated that the OFF-to-ON SERS system using RHB immobilized on silver-coated gold nanobowls permitted rapid hybridization. This proof-of-concept could provide a potential diagnostic tool for point-ofcare influenza virus detection.

Original language	English
Pages (from-to)	2352-2360
Number of pages	9
Journal	Optical Materials Express
Volume	7
Issue number	7
DOIs	https://doi.org/10.1364/OME.7.002352
Publication status	Published - 2017

Bibliographical note

Funding Information:
BioNano Health-Guard Research Center funded by the Ministry of Science, ICT and Future Planning (MSIP) of Korea as the "Global Frontier Project" (grant no. HGUARD_ 2013M3A6B2078946).

Publisher Copyright:
© 2017 Optical Society of America.

All Science Journal Classification (ASJC) codes

Electronic, Optical and Magnetic Materials

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10.1364/OME.7.002352

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title = "Optimal DNA structure of reverse-hairpin beacons for label-free and positive surface enhanced Raman scattering assays",

abstract = "We developed a label-free and positive-readout surface enhanced Raman scattering (SERS) assay using reverse-hairpin molecular beacons (RHBs) for the detection of RNA genetic markers associated with a high pathogenicity influenza (HPAI) virus. The structure of RHBs flexibly changed from a linear configuration (open state) to hairpin (closed state) upon targeting, such that the Raman label was closed on the SERS substrate and induced an increase of SERS intensity (OFF-to-ON). By improving sequence-specific RNA/DNA hybridization efficiency, we adjusted the stem-loop ratio of RHB, which was efficient at values of less than 1. The optimized RHBs exhibited dramatic changes in signal based on a fluorescence system in which the target was present. We demonstrated that the OFF-to-ON SERS system using RHB immobilized on silver-coated gold nanobowls permitted rapid hybridization. This proof-of-concept could provide a potential diagnostic tool for point-ofcare influenza virus detection.",

author = "Jisun Ki and Jinyoung Kim and Seeungmin Han and Eunji Jang and Taeksu Lee and Wi, {Jung Sub} and Lee, {Tae Geol} and Woonsung Na and Daesub Song and Seungjoo Haam",

note = "Funding Information: BioNano Health-Guard Research Center funded by the Ministry of Science, ICT and Future Planning (MSIP) of Korea as the {"}Global Frontier Project{"} (grant no. HGUARD_ 2013M3A6B2078946). Publisher Copyright: {\textcopyright} 2017 Optical Society of America.",

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doi = "10.1364/OME.7.002352",

language = "English",

volume = "7",

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TY - JOUR

T1 - Optimal DNA structure of reverse-hairpin beacons for label-free and positive surface enhanced Raman scattering assays

AU - Ki, Jisun

AU - Kim, Jinyoung

AU - Han, Seeungmin

AU - Jang, Eunji

AU - Lee, Taeksu

AU - Wi, Jung Sub

AU - Lee, Tae Geol

AU - Na, Woonsung

AU - Song, Daesub

AU - Haam, Seungjoo

N1 - Funding Information: BioNano Health-Guard Research Center funded by the Ministry of Science, ICT and Future Planning (MSIP) of Korea as the "Global Frontier Project" (grant no. HGUARD_ 2013M3A6B2078946). Publisher Copyright: © 2017 Optical Society of America.

PY - 2017

Y1 - 2017

N2 - We developed a label-free and positive-readout surface enhanced Raman scattering (SERS) assay using reverse-hairpin molecular beacons (RHBs) for the detection of RNA genetic markers associated with a high pathogenicity influenza (HPAI) virus. The structure of RHBs flexibly changed from a linear configuration (open state) to hairpin (closed state) upon targeting, such that the Raman label was closed on the SERS substrate and induced an increase of SERS intensity (OFF-to-ON). By improving sequence-specific RNA/DNA hybridization efficiency, we adjusted the stem-loop ratio of RHB, which was efficient at values of less than 1. The optimized RHBs exhibited dramatic changes in signal based on a fluorescence system in which the target was present. We demonstrated that the OFF-to-ON SERS system using RHB immobilized on silver-coated gold nanobowls permitted rapid hybridization. This proof-of-concept could provide a potential diagnostic tool for point-ofcare influenza virus detection.

AB - We developed a label-free and positive-readout surface enhanced Raman scattering (SERS) assay using reverse-hairpin molecular beacons (RHBs) for the detection of RNA genetic markers associated with a high pathogenicity influenza (HPAI) virus. The structure of RHBs flexibly changed from a linear configuration (open state) to hairpin (closed state) upon targeting, such that the Raman label was closed on the SERS substrate and induced an increase of SERS intensity (OFF-to-ON). By improving sequence-specific RNA/DNA hybridization efficiency, we adjusted the stem-loop ratio of RHB, which was efficient at values of less than 1. The optimized RHBs exhibited dramatic changes in signal based on a fluorescence system in which the target was present. We demonstrated that the OFF-to-ON SERS system using RHB immobilized on silver-coated gold nanobowls permitted rapid hybridization. This proof-of-concept could provide a potential diagnostic tool for point-ofcare influenza virus detection.

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Optimal DNA structure of reverse-hairpin beacons for label-free and positive surface enhanced Raman scattering assays

Abstract

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