Sequence selectivity of DNA damage

Molecular Life Sciences (2014)


Different reactive molecules prefer to react at different sites within strands of DNA, due to electronic and base-stacking effects.


Different chemicals react with different bases and at different atoms on them, as discussed under “fi Selectivity of Chemicals for DNA Damage.” In addition, damage is usually not random, and some selectivity is seen along the DNA depending upon neighboring effects. The selectivity varies for different types of damage and may or may not predict mutational spectra.

Damage by hydroxyl radicals (OH•) is very nonselective because of the very short lifetime of the species (Fig. 1). Therefore, hydroxyl radicals can be used in “footprinting” for agents that generate OH•. Dimethyl sulfate has also been used as a footprinting agent because of its nonselective reactivity.

Some of the larger, more complex drugs show considerable sequence selectivity (Fig. 1; Hurley et al 1988).

Some compounds bind in the major groove of DNA and some in the minor. However, this difference does not have a pronounced effect on sequence selectivity in that the grooves are continuous in fi-DNA. However, certain compounds may target regions of DNA that adopt unusual forms. For example, chloroacetaldehyde has been reported to preferentially cross-link regions of Z-DNA. There is interest in developing drugs that will specifically bind to the G-quadruplex regions of telomeres for cancer therapy.

For the majority of carcinogens, there is modest sequence selectivity. Our experience is that there is generally <10-fold difference. In some cases the selectivity is the result of intercalation of aromatic rings between purines, e.g., with aflatoxin B1 (Iyer et al. 1994).

In general, the sequence selectivity for forming cross-links is greater than for “mono”-adduct formation, in that the initial binding event occurs, but the second is highly dependent upon achieving the correct distance for completing the cross-link.

A number of attempts have been made to devise paradigms for the sequence selectivity of bindings of certain carcinogens. However, these have not proven to be reliable. Several comparisons have been made between sites of modification and mutation. There is some evidence for such a relationship with the p53 gene and cancer (Denissenko et al. 1996), although one might not expect an exact relationship. An investigation with the half-mustard formed from glutathione and ethylene dibromide did not show a good relationship between the initial sites of adduction and mutation in a human p53 yeast system (Fig. 2; Valadez and Guengerich 2004). However, much better correlation was seen for mutation sites with the DNA alkylation pattern obtained 24–48 h after treatment, suggesting that the sequence selectivity of DNA repair is more of an issue than the initial chemical selectivity. Another point is that DNA polymerases are known to differ in their proclivity to copy past (and miscode at) different sequences. Also, frameshift mutations are more prone to sequence selectivity (than base pairs) because of processes such as slippage that depend on transient pairing.

Sequence selectivity of DNA damage 1

Fig. 1. Comparisons of the complexity of two DNA-modifying agents, the drug CC-1065 and hydroxy radical

Sequence selectivity of DNA damage 2

Fig. 2. Sequence selectivity of DNA damage and mutation in DNA (exon five of human p53 gene) (Valadez and Guengerich 2004). (a) Mapping of sites of initial damage by LMPCR. (b) Sites of base-pair mutations, determined by sequencing


Denissenko MF, Pao A, Tang M et al (1996) Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in p53. Science 274:430–432

Hurley LH, Lee CS, McGovren JP et al (1988) Molecular basis for sequence-specific DNA alkylation by CC-1065. Biochemistry 27:3886–3892

Iyer R, Coles B, Raney KD et al (1994) DNA adduction by the potent carcinogen afiatoxin B1: mechanistic studies. J Am Chem Soc 116:1603–1609

Valadez JG, Guengerich FP (2004) S-(2-Chloroethyl)glutathione-generated p53 mutation spectra are infiuenced by differential repair rates more than sites of initial DNA damage. J Biol Chem 279:13435–13446



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