The SAM is the most labile component of the reaction. If the stock solution is older than 6 months it should be replaced. If more than 1 μg of DNA is being methylated, increase the SAM concentration from the recommended 160 μM to 640 μM. A maximum of 4 μg per 20 μls reaction can be methylated using 640 μM SAM. Use 2-4 units per microgram. Use concentrated SssI M0226M to keep glycerol concentration low. Increase the reaction time to 4 hours. Due to SAM instability and the fact that the byproduct of the reaction (S-adenosylhomocysteine) is an inhibitor overnight reactions are not recommended. Clean up the DNA. Remove PCR primers and other small DNA using a spin column or similar procedure. Drop dialyze the sample to remove salts.