- Chemical Mutagens
- Base analogs mimic the normal DNA bases, but don't pair as faithfully as the real thing.
- 5-Bromo Uracil: Thymine analog, has Br instead of methyl group. Br is powerfully electronegative, so chances the charge dynamics of the base, and thus the H-bonding behavior, even though the Br isn't involved in the pairing.
- 2-amino-purine: Adenine analog.
- Base-altering chemicals change the bases themselves and alter pairing properties. For example, Alkylating agents (eg nitrosoguanidine) chemically alter bases by adding an alkyl group (such as a methyl group) to a variety of places on the bases.
- Intercalating agents are planar molecules which slip between the stacked nucleotides of replicating DNA and cause single base insertions and deletions. Examples: proflavin, acridine orange.
- Ultraviolet (a non-ionizing radiation) causes formation of pyrimidine dimers. These cause pairing problems, as the dimer involves the parts of the pyrimidine base which normally participate in the hydrogen bonding which creates base pairing, and because the dimer compresses the two-base portion of the polynucleotide, thus causing the possibility of only one base, rather then the required two, being inserted in the newly constructed strand.
- Ionizing radiation (such as X-Rays or gamma rays) can directly damage the DNA itself, or can ionize and excite components of the aqueous environment around the DNA, generating hydroxyl groups, oxygen radicals and hydrogen peroxide, which can cause secondary damage to the DNA.