Label-free detection of DNA methylation by surface-enhanced Raman spectroscopy using zirconium-modified silver nanoparticles

DNA methylation is an important feature of gene epigenetics that affects the metabolic process of organisms. Although surface-enhanced Raman spectroscopy (SERS) has demonstrated great potential in label-free DNA detection, discriminating the various processes involved in DNA methylation remains a challenge. DNA molecules fold themselves, wrapping the hydrophobic bases, thus making it difficult for traditional methods to detect single-base signals. In this study, we develop a SERS platform for detecting DNA via modifying silver nanoparticles by zirconium ions to obtain the DNA fingerprint information of base methylations (N6-methylated adenine and 5-methylated cytosine). Zirconium ions open the folded DNA molecules, enabling SERS signals of the four DNA bases (A, C, G, T) to be obtained as well as identification of the subtle differences between normal and methylated DNA with single base-level sensitivity. Moreover, the identifying information of DNA methylation was obtained by combining principal component analysis (PCA) with 2D correlation spectroscopy analysis. The findings of this study provide a substantial progress for current platforms for DNA sequencing, genetic testing, and gene-disease treatment.