Epigenetic events such as DNA methylation play important roles in the regulation of gene expression. DNA methylation patterns have been found to differ between healthy and diseased tissue, such as healthy and cancerous tissue, thereby allowing DNA methylation to serve as a biomarker for disease states. Embodiments of the invention provide methods for detecting methylation patterns in DNA polymers. Methylation patterns are detected, in part, through the use of surface enhanced Raman spectroscopy (SERS). SERS provides a sensitive structure-based technique for chemical analysis.