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

Abstract

Purpose : 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. Materials and methods : Monolayers of homogeneous nonamers of deoxycytidine and thymidine (dCy 9 and T 9) and heterogeneous nonamers of thymidine substituted with 33 and 66% of deoxycytidine (dCy 3 -T 6 and dCy 6 -T 3) 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. Results : CN, OCN and/or H 2 NCN were the major neutral species observed to desorb in the present experiments. A small contribution of 55 amu neutral species, tentatively attributed to CH 3 CCO, were only detected from fragmentation of oligonucleotides containing thymine. The total ECS per base estimated for the CN, OCN and CH 3 CCO species production from fragmentation of dCy 9, dCy 6 -T 3, dCy 3 -T 6 and T 9 at 12 eV incident electron energy were (3.4, 2.0, 2.9 and 2.3) ×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. Conclusions : 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.