Weaver/Molecular Biology

Damage Caused by Alkylation of Bases

Some substances in our environment, both natural and synthetic, are electrophilic. This name means electron- (or negative charge-) loving; thus, electrophiles seek centers of negative charge in other molecules and bind to them. Many other environmental substances are metabolized in the body to electrophilic compounds. One of the most obvious centers of negative charge in biology is the DNA molecule. Every nucleotide contains one full negative charge on the phosphate and partial negative charges on the bases. When electrophiles encounter these negative centers, they attack them, usually adding carbon-containing groups called alkyl groups. Thus, we refer to this process as alkylation.

Aside from the phosphodiester bonds, the favorite sites of attack by alkylating agents are the N7 of guanine and the N3 of adenine (Figure 1). Since neither of these positions is involved in base-pairing, such alkylations do not lead immediately to mispairing. However, they do make the bond between sugar and base more labile, or more apt to break. When this break occurs, it leaves an apurinic site, a sugar without its purine. This obviously cannot be replicated properly unless it is first repaired, but cells sometimes attempt to replicate apurinic DNA anyway. If they do, they frequently insert the wrong base across from an apurinic site, and this generates a mutation. Alkylation can also enhance the tendency of a base to form the rare (wrong) tautomer, which changes the base-pairing properties, leading to mutations. Moreover, all of the nitrogen and oxygen atoms involved in base-pairing are also subject to alkylation, which can directly disrupt base-pairing and lead to mutation (Figure 2).

Many environmental carcinogens, or cancer-causing agents, are electrophiles that act by attacking DNA and alkylating it. Many of the favorite mutagens used in the laboratory for the express purpose of creating mutations are also alkylating agents. One example is ethylmethane sulfonate (EMS), which transfers ethyl (CH₃-CH₂) groups to DNA (Figure 2).

Summary: Alkylating agents like ethylmethane sulfonate add bulky alkyl groups to bases, either disrupting base-pairing directly or causing loss of bases, either of which can lead to faulty DNA replication or repair.

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