Important effects of neighbouring nucleotides on electron induced DNA single-strand breaks

In this Letter, we present Quantum Mechanics/Molecular Mechanics (QM/MM) calculations on molecules containing a 2-deoxycytidine-3′-monophosphate moiety (3′-dCMPH). In particular, we examine the effect that including neighbouring nucleotides at the Molecular Mechanic (MM) level has on the calculated electron affinities and on the energetic barriers of the C3′–O3′ bond cleavage. Our results demonstrate that the surrounding nucleotides relocate the excess electron from the π∗ orbital of the base to a diffuse phosphate-centred orbital, leading to the formation of a dipole-bound anion state. Both the electron affinities and the activation energy of C3′–O3′ bond cleavage are strongly increased.