A variation of DNAse footprinting in which certain residues are methylated to evidence their role in binding. Similar to site-directed mutagenesis in its ability to designate specific residues as being essential for binding.

Primer Extension Assay is a simple method of assessing expression levels. The total RNA produced by the culture is isolated. A short synthetic oligonucleotide primer (complementary to a short sequence on the target RNA) is radiolabelled (usually with 32P) and the primer anneals to the RNA. Reverse transcriptase then extends the RNA producing cDNA. The cDNA is analyzed on a polyacrylamide gel. The amount of cDNA in a band on the gel is proportional to the amount of initial RNA, thus providing expression levels of RNA from the culture.

Visual inspection of promoter region to identify putative binding sites based on previous knowledge