Photochemical Generation of a C5′-Uridinyl Radical

Strand Breaks Induced by Very Low Energy Electrons: Product Analysis and Mechanistic Insight into the Reaction with TpT

Numerous experimental studies show that 5-15 eV electrons induce strand breaks in DNA at energies below the ionization threshold of DNA components. In this energy range, DNA damage arises principally by the formation of transient negative ions, decaying into dissociative electron attachment (DEA) and electronic excitation of dissociative states. Here, we carried out LC-MS/MS analysis of the degradation products arising from bombardment of TpT, a DNA model compound, irradiated with very low energy electrons (vLEEs; ∼1.8 eV). The formation of thymidine 5'-monophosphate (TMP5') together with 2',3'-dideoxythymidine (ddT3') can be explained by cleavage of the C3'-O bond of TpT, whereas thymidine 3'-monophosphate (TMP3') and 2',5'-dideoxythymidine (ddT5') are formed by cleavage of the C5'-O bond. The formation of ddT3' and ddT5' decreased upon irradiation of either TMP5' or TMP3', and even further in the case of thymidine, underlining the critical role of the phosphate group. Interestingly, the yield of TMP5' and TMP3' was higher than that of the corresponding ddT3' and ddT5' products, suggesting alternative fates of C3' and C5'-centered sugar radicals. In contrast, the release of thymine from TpT was minor (<20%) and did not result in the formation of expected products from DEA-mediated cleavage at the N-glycosidic bond. Lastly, vLEE induced the conversion of thymine to 5,6-dihydrothymine (5,6-dhT) within TpT, a reaction likely involving thymine anion radicals. In summary, we show that a major pathway of vLEEs involves DEA-mediated cleavage of the C3'-O and C5'-O bonds of TpT, resulting in the formation of specific fragments, which represent a prompt single strand break in DNA.

Aminyl Radical Generation via Tandem Norrish Type I Photocleavage, β-Fragmentation: Independent Generation and Reactivity of the 2'-Deoxyadenosin- N6-yl Radical

Formal hydrogen atom abstraction from the nitrogen-hydrogen bonds in purine nucleosides produces reactive intermediates that are important in nucleic acid oxidation. Herein we describe an approach for the independent generation of the purine radical resulting from hydrogen atom abstraction from the N6-amine of 2'-deoxyadenosine (dA•). The method involves sequential Norrish Type I photocleavage of a ketone (7b) and β-fragmentation of the initially formed alkyl radical (8b) to form dA• and acetone. The formation of dA• was followed by laser flash photolysis, which yields a transient with λ_max ≈ 340 nm and a broader weaker absorption centered at ∼560 nm. This transient grows in at ≥2 × 10⁵ s^-1; however, computations and reactivity data suggest that β-fragmentation occurs much faster, implying the consumption of dA• as it is formed. Continuous photolysis of 7b in the presence of ferrous ion or thiophenol produces good yields of dA, whereas less reactive thiols afford lower yields presumably due to a polarity mismatch. This tandem photochemical, β-fragmentation method promises to be useful for site-specific production of dA• in nucleic acid oligomers and/or polymers and also for the production of aminyl radicals, in general.

Reactivity of Nucleic Acid Radicals

Nucleic acid oxidation plays a vital role in the etiology and treatment of diseases, as well as aging. Reagents that oxidize nucleic acids are also useful probes of the biopolymers' structure and folding. Radiation scientists have contributed greatly to our understanding of nucleic acid oxidation using a variety of techniques. During the past two decades organic chemists have applied the tools of synthetic and mechanistic chemistry to independently generate and study the reactive intermediates produced by ionizing radiation and other nucleic acid damaging agents. This approach has facilitated resolving mechanistic controversies and lead to the discovery of new reactive processes.