||This reaction is usually very clean, but it is the reaction most sensitive to prolonged incubation and to the quality of the reactive reagent, DMS. If reaction proceeds longer than the allotted time or if old or bad quality dimethyl sulfate is used, excessive and nonspecific degradation of DNA will occur.
||This is usually a trouble-free reaction.
|CT and C reactions
||The quality of the hydrazine should be good (it does not have to be exceptional), otherwise excessive and nonspecific degradation will occur. Sometimes faint bands will be seen in the C and CT lanes when the base is G (a strong band is then observed in the G lane). The likely explanation is that the pH in the reaction tubes is too low (there is no buffer in the C and CT reaction tubes, but carryover with the DNA sample might cause this to happen). However, these faint bands are not nearly as strong as the signal in the G lane or as bona fide bands of C and T bases.