Abstract: Provided herein are methods for mapping modified nucleotide residues in nucleic acids. The methods include providing a nucleic acid sample in which non-target or target modified and unmodified nucleotide residues are converted to form of a different nucleotide (such a “C” being converted to “T”). Second strand synthesis is then performed on the converted nucleic acids using a set of anchored-base primers. Each primer in the set of anchored-base primers comprises one or more anchor bases at the 3? terminus that are complementary to the target nucleotide (e.g., “G” or “CpG”), and a sequence of nucleotides selected from a set of sequences that could be a fully or partially degenerate set of sequences. For example, the sequence could be 5?-XnG-3? and/or 5?-X(n?1)CG-3?, wherein X is any base, and n=2 to 25. Double-stranded nucleic acid products can be analyzed, for example by amplification and high throughput sequencing.

Abstract: Provided herein is a new molecular marker in DNA: N-4-acetyldeoxycytidine (“N4-acdC”). Also provided herein are methods of detecting N4-acdC residues in DNA molecules as well as methods of using detected N4-acdC residues, for example in genetic mapping and diagnostics.