Plasmonic Gold Nanohole Array for Surface-Enhanced Raman Scattering Detection of DNA Methylation

Abstract

Surface-enhanced Raman spectroscopy (SERS), which utilizes nanogaps between noble-metal nanostructures as hot spots to yield ultrasensitive SERS signals, is an outstanding label-free and straightforward tool for DNA methylation analysis. Herein, a plasmonic gold nanohole array (PGNA) with well-controlled hot spots and an open surface was designed as a SERS substrate for DNA methylation detection. A finite-difference time-domain (FDTD) simulation was first employed to investigate the electric field distributions of the PGNA as a function of the geometric parameters. The plasmonic response was tuned to 785 cm −1 to match the ring breathing vibrational band of cytosine, the intensity change of which was revealed to be a marker of DNA methylation. Then, guided by the FDTD simulation results, the PGNA was fabricated via the electron beam lithography (EBL) technique. The fabricated PGNA had an open and easily accessible surface topology, a SERS enhancement factor of ∼10 6 , and a relative standard deviation (RSD) of 7.1% for 500 repetitions over an area of 20 × 20 μm 2 using 1 μM Rhodamine 6G as the Raman reporter. The fabricated PGNA was further used as a platform for determining DNA methylation. The proposed method exhibited a sensitivity for detecting 1% of methylation changes. Moreover, insight into the dynamic information on methylation events was obtained by combining principal component analysis (PCA) with 2D correlation spectroscopy analysis. Finally, clear discrimination of the different methylation sites, such as 5-methylcytosine and N6-methyladenine, was demonstrated.

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

“…23 However, in substrates prepared by templates or lithography methods, it is easy to tune their SPR properties. For example, we previously fabricated a structured substrate with a subwavelength round gold nanoholes array via the electron beam lithography (EBL) technique, 24,25 which showed a tunable SPR property. The intensity and the location of its SPR depended sensitively on the structure of the array.…”

Plasmonic-Active Nanostructured Thin Films

“…The PMMA works as a support for the nanohole array and is not removed. Recently, this strategy was utilized by Luo et al for preparing plasmonic-active nanohole array having SERS enhancement factor (E) = ~10 6 and used it to determine DNA methylation [61]. EBL can also be used for etching and creating nanohole array on substrate, which can then be used for creating plasmonic active thin film nanohole array by direct deposition of plasmonic material.…”

Biosensors for Studies on Adhesion-Mediated Cellular Responses to Their Microenvironment

“…Cells can be seeded on SERS substrates, and once they adhered and spread, their chemical composition near the surface can be studied by irradiating the substrate and measuring the Raman spectra. Over the years, a wide diversity of metal nanostructured surfaces have been created for SERS, such as nanoparticles attached to a surface (Freeman et al, 1995;Zhai et al, 2009;Lussier et al, 2016), nanopillars (Kang et al, 2015;Li et al, 2016), nanoholes (Abdelsalam et al, 2005;Luo et al, 2019), and others (Yüksel et al, 2017;Yao et al, 2020). A detailed review on the fabrication of SERS substrates can be found in Fan et al (2011).…”