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Influence of the Au cluster enhancer on vibrational spectra of nucleotides in MD simulation of a SERS sensor
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1  Department of Mechanical Engineering, University of Toyama, Toyama 930-8555, Japan

https://doi.org/10.3390/IECB2020-07076 (registering DOI)
Abstract:

Recently, surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in oncological imaging owing to the high sensitivity and specificity of their fingerprint-like spectra. As current Raman scanners rely on a slow, point-by-point spectrum acquisition, there is an unmet need for faster imaging in real-time. The development of single-molecule resolution in the tip-enhanced and surface-enhanced Raman spectroscopy (TERS & SERS) promotes experimental work on DNA and protein identification by the above methods and approaches a single oligomer resolution that leads to its use as a nanobiosensor. However, a weak signal requires multiple acquisitions of the averaged spectra to enhance the signal, and information on the molecular conformation and interaction is erased. The enhancer Au clusters of known geometry, size, and position relative to the measured molecule will help to build spectral libraries for single spectral signal prediction.

As the simulation molecular dynamic (MD) model of a sensing system, we study vibrational spectra of the cytosine nucleotide in the dynamic interaction with the Au20 nanoparticles (NP) that can be later attached to graphene nanopore. We define nucleotide and NP localization and study the influence of interaction on the spectral modes of both the nucleotide and NP, as we had seen in the case of the nucleotide-graphene nanopore. The spectral maps of the nucleotides were built in FF2/FF3 potential. Fourier transfer of the density of states (DOS) was performed to obtain the spectra of various bonds in reaction coordinates for DNA nucleotides at a numerical resolution 20 to 40 cm-1. The pyramid-shaped Au20 NP was optimized by ab initio DFT GGA and relaxed by the MD calculation with the EAM potential with Δt=0.1fs. Spectral maps of the Au NP were acquired for each atom. The frequencies that can serve as markers of the corresponding Au – nucleotide interaction have been evaluated.

Keywords: Vibrational spectra, nucleotides, Au nanoparticle, molecular dynamics, SERS
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