Sensitivity-Improved SERS Detection of Methyltransferase Assisted by Plasmonically Engineered Nanoholes Array and Hybridization Chain Reaction

Abstract

Detection of methyltransferase (MTase) activity is of great significance in methylation-related disease diagnosis and drug screening. Herein, we present a dual-amplification sensing strategy that is assisted by plasmonically enhanced Raman intensity at engineered nanoholes array, along with signal amplification by the hybridization chain reaction (HCR) for the ultrasensitive detection of M.SssI MTase activity and inhibitor screening. An engineered surface-enhanced Raman scattering (SERS) substrate, namely, a structured nanoholes array (NHA) with wavelengthmatched surface plasmon resonance (SPR) at the wavelength of laser excitation (785 nm), was rationally designed through finitedifference time-domain (FDTD) simulations, precisely fabricated through master-assisted replication, and then used as a sensing platform. Uniform and intense SERS signals were achieved by turning on the plasmonic enhancement under the excitation of SPR. Probe DNA was designed to hybridize with target DNA (a BRCA1 gene fragment), and the formed dsDNA with the recognition site of M.SssI was assembled on the NHA. In the presence of M.SssI, the HCR process was triggered upon adding DNAs labeled with the Raman reporter Cy5, leading to an amplified SERS signal of Cy5. The intensity of Cy5 increases with increasing M.SssI activity, which establishes the basis of the assay for M.SssI. The developed assay displays an ultrasensitivity that has a broad linear range (0.002−200 U/mL) and a low detection limit (2 × 10 −4 U/mL), which is superior to that of the reported SERS-based detection methods. Moreover, it can selectively detect M.SssI in human serum samples and evaluate the efficiency of M.SssI inhibitors.

Boosting Long-Range Surface-Enhanced Raman Scattering on Plasmonic Nanohole Arrays for Ultrasensitive Detection of MiRNA

“…The introduction of HCR into SERS-based detection improved the detection sensitivity because it brought more absorbed reporters on the SERS substrate. 36 However, the signal amplification efficiency was weak owing to the near-field effect of SERS enhancement. 37 Some reporter molecules in the chain-like DNA nanostructure located outside of the electromagnetic field (E-field) hardly contribute to the amplified SERS signal.…”

“…Among these various amplification strategies, HCR is nonenzymatic, simple in design and operation, and cost-effective, making it convenient and the most widely used. The introduction of HCR into SERS-based detection improved the detection sensitivity because it brought more absorbed reporters on the SERS substrate . However, the signal amplification efficiency was weak owing to the near-field effect of SERS enhancement .…”

Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing

“…111 Luo et al developed a novel SERS strategy at a structured nanohole array with tuned 785 nm surface plasmon resonance (SPR). 112 The substrate exhibited SERS enhancement 500 times higher than that of commercial Klarite substrate, and HCR was further applied for dual amplification for the assay of methyltransferase. Clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins systems have shown great potential in the development of advanced biosensor due to the trans-cleavage capabilities of the Cas effector proteins.…”

“…With the fingerprint signature and sharp vibrational bands, surface-enhanced Raman scattering (SERS) emerges as an important analytical technique with ultrahigh sensitivity . Luo et al developed a novel SERS strategy at a structured nanohole array with tuned 785 nm surface plasmon resonance (SPR) . The substrate exhibited SERS enhancement 500 times higher than that of commercial Klarite substrate, and HCR was further applied for dual amplification for the assay of methyltransferase.…”

Multiplexed SERS Detection of Microcystins with Aptamer-Driven Core–Satellite Assemblies

“…SERS enhancement is dominated by local amplification of the electromagnetic (EM) field . There are several methods to enhance the local EM field, such as the formation of ultrasmall gaps between plasmonic particles or between particles and tips. − It has also been reported that such gaps in core–shell structures can give rise to a large SERS enhancement of up to ∼10 11 for embedded Raman labels . These core–shell structures hold great promise for developing broadly applicable SERS tags by incorporating Raman labels as internal standards.…”