Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites

Abstract

Apurinic/apyrimidinic (AP) sites are constantly formed in cellular DNA due to instability of the glycosidic bond, particularly at purines and various oxidized, alkylated, or otherwise damaged nucleobases. AP sites are also generated by DNA glycosylases that initiate DNA base excision repair. These lesions represent a significant block to DNA replication and are extremely mutagenic. Some DNA glycosylases possess AP lyase activities that nick the DNA strand at the deoxyribose moiety via a β- or β,δ-elimination reaction. Various amines can incise AP sites via a similar mechanism, but this non-enzymatic cleavage typically requires high reagent concentrations. Herein, we describe a new class of small molecules that function at low micromolar concentrations as both β- and β,δ-elimination catalysts at AP sites. Structure-activity relationships have established several characteristics that appear to be necessary for the formation of an iminium ion intermediate that self-catalyzes the elimination at the deoxyribose ring.

Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand–DNA Adducts

“…Furthermore, the product was stable towards brief heating at 90 °C (Figure a, lane 4), which speaks in favor of the covalent modification of DNA. Next, we performed a trapping reaction through the incubation of 17‐TX with 2,7‐BisNP‐NH under the conditions of reductive amination (NaCNBH 3 , followed by NaBH 4 quenching; Figure a, lane 5) . In this case, we found evidence of the formation of a slower‐migrating band (*** in Figure a), which supposedly corresponded to the reduced preincision iminium base intermediate (cf.…”

“…However, in parallel to inhibiting APE1 activity, polyazacyclophane ligands also induce an enzyme‐independent cleavage of AP sites through a β‐elimination mechanism, due to the presence of secondary amino groups in the ligand structure (Scheme , bottom) . The latter process, reminiscent of the action of AP lyases (class I endonucleases), was also observed for oligopeptides KWK and KWKK, as well as several other small‐molecule ligands endowed with primary or secondary amino groups, eponymously termed “artificial AP lyases” . It has been proposed that such molecules may interfere with the normal BER process because of the accumulation of “dirty ends” (products of β‐ and β,δ‐elimination) that cannot be utilized as substrates by DNA polymerases, and therefore, also increase the cytotoxic effect of DNA‐alkylating drugs …”

Interstrand cross-links arising from strand breaks at true abasic sites in duplex DNA

“…Nicked DNA duplexes containing the 3’ddR5p end group at the break were generated by reaction of the endogenous polyamine spermine ( 60 ) with the corresponding Ap duplexes ( 43 , 45 , 61 ). The 5’- 32 P-labeled, 35 base pair Ap-containing duplex A (Figure 1 ) was prepared from the corresponding 2’-deoxyuridine-containing duplex by treatment with uracil DNA glycosylase (UDG) as described previously ( 53 – 58 , 62 – 64 ).…”

“…Nicked duplex C, containing the 3’ddR5p end group was generated by addition of spermine (1 mM), to the UDG reaction ( 43 , 45 , 61 ). Spermine is an endogenous polyamine that is present at millimolar concentrations in the nuclei of cells ( 60 ).…”

AOP report: Development of an adverse outcome pathway for oxidative DNA damage leading to mutations and chromosomal aberrations

“…DNA glycosylases remove oxidized nitrogenous bases by hydrolyzing the N-glycosidic bond, giving rise to an abasic site (AP). The lyase function of bifunctional glycosylases creates a SSB 3 0 to the AP site after the removal of the oxidized nitrogenous base (Jacobs & Schar, 2012;Minko et al, 2016).…”