Maybe use HPLC, we used （1994-1996）HPLC to analize the fully digestion of a single strand DNA to find out the ratio of dA/dC/dG/T. During the digestion, you can see different fragments with phosphates. For modified base, sometimes digestion was slow or need diffenent combination of enzymes.

Good luck！

Thank you Mr. Xiang.

can you share the protocol for the digestion ?

please read my publications 1994（JACS） and 1996 （Nuclic Acid Research），1998 （Tetrahedron）。But they were all for DNA。