Electron attachment to DNA single strands: gas phase and aqueous solution.
The 2'-deoxyguanosine-3',5'-diphosphate, 2'-deoxyadenosine-3',5'-diphosphate, 2'-deoxycytidine-3',5'-diphosphate and 2'-deoxythymidine-3',5'-diphosphate systems are the smallest units of a DNA single strand. Exploring these comprehensive subunits with reliable density functional methods enables one to approach reasonable predictions of the properties of DNA single strands. With these models, DNA single strands are found to have a strong tendency to capture low-energy electrons. The vertical attachment energies (VEAs) predicted for 3',5'-dTDP (0.17 eV) and 3',5'-dGDP (0.14 eV) indicate that both the thymine-rich and the guanine-rich DNA single strands have the ability to capture electrons. The adiabatic electron affinities (AEAs) of the nucleotides considered here range from 0.22 to 0.52 eV and follow the order 3',5'-dTDP > 3',5'-dCDP > 3',5'-dGDP > 3',5'-dADP. A substantial increase in the AEA is observed compared to that of the corresponding nucleic acid bases and the corresponding nucleosides. Furthermore, aqueous solution simulations dramatically increase the electron attracting properties of the DNA single strands. The present investigation illustrates that in the gas phase, the excess electron is situated both on the nucleobase and on the phosphate moiety for DNA single strands. However, the distribution of the extra negative charge is uneven. The attached electron favors the base moiety for the pyrimidine, while it prefers the 3'-phosphate subunit for the purine DNA single strands. In contrast, the attached electron is tightly bound to the base fragment for the cytidine, thymidine and adenosine nucleotides, while it almost exclusively resides in the vicinity of the 3'-phosphate group for the guanosine nucleotides due to the solvent effects. The comparatively low vertical detachment energies (VDEs) predicted for 3',5'-dADP(-) (0.26 eV) and 3',5'-dGDP(-) (0.32 eV) indicate that electron detachment might compete with reactions having high activation barriers such as glycosidic bond breakage. However, the radical anions of the pyrimidine nucleotides with high VDE are expected to be electronically stable. Thus the base-centered radical anions of the pyrimidine nucleotides might be the possible intermediates for DNA single-strand breakage.
Gu
Jiande
J
Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, PR China. jiandegush@go.com
Xie
Yaoming
Y
Schaefer
Henry F
HF
D000244:Adenosine Diphosphate / Q000031:analogs & derivatives / Q000737:chemistry; D000838:Anions / Q000737:chemistry; D053904:DNA Breaks, Single-Stranded; D004277:DNA, Single-Stranded / Q000737:chemistry*; D003845:Deoxycytosine Nucleotides / Q000737:chemistry; D004583:Electrons; D005740:Gases / Q000737:chemistry; D006153:Guanosine Diphosphate / Q000031:analogs & derivatives / Q000737:chemistry; D008958:Models, Molecular; D012997:Solvents / Q000737:chemistry; D013942:Thymine Nucleotides / Q000737:chemistry; D014867:Water / Q000737:chemistry
C523304:2'-deoxyadenosine-3',5'-diphosphate; C523305:2'-deoxythymidine-3',5'-diphosphate; D000838:Anions; D004277:DNA, Single-Stranded; D003845:Deoxycytosine Nucleotides; D005740:Gases; D012997:Solvents; D013942:Thymine Nucleotides; D014867:Water; D006153:Guanosine Diphosphate; C065276:2'-deoxyguanosine 3',5'-diphosphate; C059281:2'-deoxycytidine 3',5'-diphosphate; D000244:Adenosine Diphosphate