Fragmentation of short single DNA strands by 1-30 eV electrons: dependence on base identity and sequence

To investigate the dependence of base identity and sequence on the damage induced by low-energy (1-30 eV) electron impact on a short single strand of DNA.

Monolayers of homogeneous nonamers of deoxycytidine and thymidine (dCy9 and T9) and heterogeneous nonamers of thymidine substituted with 33 and 66% of deoxycytidine (dCy3-T6 and dCy6-T3) were chemisorbed onto a gold substrate. They were bombarded under ultrahigh vacuum conditions by a 1-30 eV electron beam. Neutral fragments desorbed from the films were detected by a mass spectrometer. From partial pressure measurements, the effective cross-section (ECS) per base for desorption of various fragments was estimated.

CN, OCN and/or H2NCN were the major neutral species observed to desorb in the present experiments. A small contribution of 55 amu neutral species, tentatively attributed to CH3CCO, were only detected from fragmentation of oligonucleotides containing thymine. The total ECS per base estimated for the CN, OCN and CH3CCO species production from fragmentation of dCy9, dCy6-T3, dCy3-T6 and T9 at 12 eV incident electron energy were (3.4, 2.0, 2.9 and 2.3) x 10(-17) cm(2), respectively. The incident electron energy dependence of ECS for desorption of these fragments exhibited structures <20 eV, which are characteristic of transient anion formation.

At incident electron energies <20 eV, neutral fragment desorption arise from dissociation of the DNA bases, principally via dissociative electron attachment and/or decay of the transient anion into a dissociative electronic excited state of the base. Non-resonant mechanisms (e.g. direct dipolar dissociation) mostly control the fragmentation processes >20 eV. From comparison of the electron energy dependence of the ECS for base fragmentation in the homo- and heteronucleotides, it is concluded that damage to a short DNA strand is dependent on base identity, sequence and electron energy.