Tip-enhanced Raman Spectroscopy Study Of RNA Strands Of SARS-CoV-2

The emergence of novel coronavirus disease in 2019(SARS-CoV-2)had dramatically changed people’s daily life,causing more than 600 million cases and 6million deaths in the whole world.Differing from deoxyribonucleic acid(DNA)molecules in cells,adenine(A),guanine(G),cytosine(C)and thymine(T)are encoded as RNA molecular chains in SARS-CoV-2 particles.Fully understanding of the RNA molecular structure and function of virus is essential to understand the infection process of SARS-CoV-2 in human cells.Among a variety of approaches enabling RNA single-base sequencing,nanopore-based sequencing methods had become representative of third-generation sequencing methods.However,single base enzyme has a shorter dwelling time in the nanopore,which leaves the method limited by poor signal.In recent years,tip-enhanced Raman spectroscopy(TERS)had become a powerful analytical tool for characterizing various nucleobase nanoparticles,viruses,and bacteria.In this study,the TERS technology was used to image the RNA fragments isolated by SARS-CoV-2 at nanoscale.The major research contents and related conclusions are as following:1)TERS measurements were conducted on the four standard nucleobase(A,T,G and C)samples.The obtained results indicate that the peak position and peak intensity of the TERS spectrum measured by the TERS probe at different positions on the nucleod particles change greatly.In order to explain the above phenomenon,by using first principle calculations,possible geometric structural models of gold / silver atoms acting at different positions of the four nucleobases (A,T,G,C)was established,and the Raman intensity of different vibration modes was calculated.The calculated results indicate that the metal atoms change the length of the bond at different absorbtion sites on the nucelobase,leading to a distinct change in the Raman intensity of different vibrational modes.These results agree well with the TERS spectral changes obtained at different positions on the nucleod particles.2)Far-field Raman spectroscopy measurements of the four standard nucleoacid(A,T,G,C)samples and pseudovirus particles were conducted.According to the Raman spectra of the four standard nucleobases,the far-field Raman spectra of pseudovirus particles containing four nucleobases(A,T,G,C)were identified,and preliminary assignment was completed.Nanoscale resolution imaging of SARS-CoV-2 RNA particles using TERS at ambient temperature was successfully conducted.The difficulty of relatively large changes in TERS spectra for conspecific nucleobases can determine the nucleobase types at different positions by calculating the minimum root mean square error of the TERS peak positions refering to those of the standard TERS A,T,G and C bases.The loci of genetic fragment was identified by searching the Gen Bank database.