Machine learning for composition analysis of ssDNA using chemical enhancement in SERS

Abstract

Surface-enhanced Raman spectroscopy (SERS) is an attractive method for bio-chemical sensing due to its potential for single molecule sensitivity and the prospect of DNA composition analysis. In this manuscript we leverage metal specific chemical enhancement effect to detect differences in SERS spectra of 200-base length single-stranded DNA (ssDNA) molecules adsorbed on gold or silver nanorod substrates, and then develop and train a linear regression as well as neural network models to predict the composition of ssDNA. Our results indicate that employing substrates of different metals that host a given adsorbed molecule leads to distinct SERS spectra, allowing to probe metal-molecule interactions under distinct chemical enhancement regimes. Leveraging this difference and combining spectra from different metals as an input for PCA (Principal Component Analysis) and NN (Neural Network) models, allows to significantly lower the detection errors compared to manual feature-choosing analysis as well as compared to the case where data from single metal is used. Furthermore, we show that NN model provides superior performance in the presence of complex noise and data dispersion factors that affect SERS signals collected from metal substrates fabricated on different days.

The effect of DNA bases permutation on surface-enhanced Raman scattering spectrum

“…Interestingly, unlike the case presented in Figures 5 and 6 above, where differences between group (1) sequences are less visible compared to differences between group (2) sequences, in this case the differences between group (2) sequences is more visible compared to group (1) sequences. We attribute this difference to more prominent CE effect of adenine bases reported in the recent work [41].…”

“…Figure S2 in the Supplementary Material section describes SEM images of a typical nanorod array used in our experiments. The metal nanorod arrays, which were used to eliminate charge transfer CE effect, were covered with 2-nm-thick Al 2 O 3 film using Atomic Layer Deposition (ALD); see the study by Nguyen et al [41] for fabrication details and also sample preparation steps. Briefly, the ssDNA solutions were prepared by diluting the DNA stock solution in 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) and MgCl 2 .…”

The effect of DNA bases permutation on surface enhanced Raman scattering spectrum

“…We attribute this difference to more prominent CE effect of adenine bases reported in the recent work [41].…”

Recent Advances in Surface-Enhanced Raman Scattering Magnetic Plasmonic Particles for Bioapplications

“…Beyond this, there are many reports that have discussed the application of machine and artificial intelligence in the SERS technique [ 145 , 146 , 147 , 148 ]. It has provided a novel idea that it is possible for artificial intelligence which learns using MPPs in bioapplication to raise a new approach in future chemistry.…”