Surface-enhanced Raman scattering for DNA methylation analysis: advances and strategies

DNA methylation, particularly the 5-methylcytosine modification, is the most prominent epigenetic modulation as it controls the expression of numerous genes in both healthy and diseased individuals. This has inspired the development of multiple diagnosis methods using DNA methylation as a cancer biomarker. However, DNA methylation analysis has not yet been established for routine cancer diagnosis due to the lack of clinical validation. Well-known methods, such as methylation-specific polymerase chain reaction (PCR), restriction enzyme-based digestion, and affinity-based enrichment, have not yet been standardized and often vary in their accuracy, sensitivity, and specificity from laboratory to laboratory. Surface-enhanced Raman scattering (SERS) has recently emerged as an alternative tool for methylation detection as it directly identifies DNA modifications through an intrinsic vibrational fingerprint, with the potential to reach single-molecule sensitivity for specific analytes under optimized conditions. Smart nanomaterial design enables orders-of-magnitude signal enhancement by optimizing probe-substrate interactions and advancing the substrate architecture. Although high-level summaries of various optical methods and comprehensive reviews of electrochemical methods have been published, this review provides, for the first time, an in-depth overview of SERS-based approaches for detecting cancer-specific DNA methylation, including their data analysis methods and potential clinical applications. The article emphasizes why SERS should be considered over existing methods as an emerging technique in DNA methylation analysis.