Someone else could probably explain it better, but the way I think of it is: intercalation is sticking something in between the 2 strands of DNA and altering the shape, therefore damaging the DNA. At the least, you hope that the DNA can't be expressed. At the best, you hope the failure of DNA repair machinery triggers the cell into apoptosis.(fat chance of that in cancer cells, though, probably) alkylation is adding an akyl group to one strand of DNA. I think doing this causes less gene expression in general. Methylation is an example of alkylation, and I know methylation decreases gene expression. In my pharm class only one of the alkylating agents, decarbazine, was listed specifically as a methylating agent.