Practice question

Incomplete cleavage leaves a heterogeneous mixture of molecules cut at different combinations of sites. Each subpopulation possesses distinct molecular weight, so upon agarose electrophoresis they separate into multiple bands of varying lengths. Instead of a sharp single fragment representing uniform cutting, a regular progression or ladder appears reflecting incremental inclusion of adjacent segments. A smear may occur if degradation is random, but partial digestion retains discrete sites, giving discrete bands. This ladder pattern is diagnostic for partial maps and useful for ordering sites.