Nearest-Neighbor Analysis

Nearest-neighbor analysis can be used to identify the 3′ nearest neighbors of 5mC residues in DNA (1,2). It can also be used to measure the level of methylation of a specific methylated dinucleotide in DNA. Typically, in the case of mammalian DNA, this means quantifying the degree of methylation at CpG dinucleotides. It has the added advantage of being applicable to small samples of the order of 1 microgram of genomic DNA. The only drawback is that it is a radioactive technique and the appropriate facilities and techniques for handling radioactive substances must be available.