DNA-base radicals. Their base pairing abilities as calculated by DFT

Abstract

The guanine radical cation (G˙⁺) deprotonates at its N1-site to give the neutral radical G(−H)˙. On the basis of DFT calculations this species is able to pair not only with cytosine (C), but also with thymine (T), adenine (A) and guanine (G), giving new base pair structures formed by the N1-site acting as a hydrogen bond acceptor. The deprotonated radical cation, G(–H)˙, forms two new (strong) hydrogen bonds with C, resulting in a new, non-classical, base pair. In contrast, pairing between G(−H)˙ and T is relatively poor. G(−H)˙ forms two hydrogen bonds with A with a similar hydrogen bond energy as the (natural) A–T base pair and it bonds with G and even with itself (G(−H)˙) forming three or two hydrogen bonds, respectively. The former has practically the same bonding energy as the (natural) G–C base pair. In summary, as compared to G, G(−H)˙ loses any specificity for C since it readily forms pairs with all the DNA bases. The deprotonated radical cation of 7,8-dihydro-8-oxoguanine, the neutral radical 8OG(–H)˙, shows very similar base pairing behavior to G(−H)˙.