These methylated and hydroxymethylated nucleotides are designed for use with epigenetic assays. The nucleotides are compatible with ZymoTaq and other DNA polymerases. They have been determined to be ultra-pure according to HPLC analysis. These reagents are free of endo/exo-deoxyribonucleases, ribonucleases, and phosphatases, human and E. coli DNA. The resultant PCR amplicons can be used in many applications including the study of binding and interacting proteins. The nucleotides are stable and guaranteed for 12 months.