Probing DNA interstrand cross-link formation by an oxidized abasic site using nonnative nucleotides

Abstract

The C4'-oxidized abasic site (C4-AP) forms two types of interstrand cross-links with the adjacent nucleotides in DNA. Previous experiments revealed that dG does not react with the lesion and that formation of one type of cross-link is catalyzed by the opposing dA. Iso-guanosine•dC and 2-aminopurine•dT base pairs were used to determine why dG does not cross-link with C4-AP despite its well known reactivity with other bis-electrophiles. 7-Deaza-2'-deoxyadenosine was used to probe the role of the nucleotide opposite C4-AP in the catalysis of interstrand cross-link formation.

Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids

“…One involves the generation of a reactive unsaturated ketoaldehyde formed upon a β-elimination reaction involving the deoxypentos-4-ulose abasic site. This reaction takes place in a sequence dependence manner since the reaction is promoted by adenine and to a lesser extent by cytosine bases located on the complementary strand [98,99]. The final product involves the formation of interstrand cross-links (ICLs) with opposite cytosine and adenine [99,100].…”

“…This reaction takes place in a sequence dependence manner since the reaction is promoted by adenine and to a lesser extent by cytosine bases located on the complementary strand [98,99]. The final product involves the formation of interstrand cross-links (ICLs) with opposite cytosine and adenine [99,100]. However, so far, the only adducts detected in cellular DNA exposed to either gamma-rays or incubated with radiomimetic bleomycin have been 2′-deoxycytidine adducts consisting of the four diastereomers of 6-(2-deoxy-β-D- erythro -pentofuranosyl)-2-hydroxy-3(3-hydroxy-2-oxopropyl)-2,6-dihydroimidazo[1,2-c]-pyrimidin-5(3 H )-one (Figure 6) [100].…”

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

“…5). Both nucleophilic bases promote beta-elimination from the acyclic form of C4 oxidized abasic sites (Sczepanski et al 2009(Sczepanski et al , 2011. The highly reactive unsaturated ketone thus generated is now able to efficiently react with opposite cytosine or adenine residues.…”

“…The mechanism of formation of ICLs involving initial † OH-mediated H-atom abstraction from the C4 of the 2-deoxyribose has been studied in certain detail (Regulus et al 2004(Regulus et al , 2007Sczepanski et al 2011). From the site-specific generation of C4 sugar radicals using a photolabile precursor, the formation of ICLs is favored by the presence of adenine on complementary DNA strands containing adenine and, to a lesser extent, cytosine (Fig.…”

Looking beneath the surface to determine what makes DNA damage deleterious

“…Depending upon the local sequence, cross-linking occurred preferentially with dC that was either opposite C4-AP or a 5′- or 3′-flanking dG. C4-AP also cross-linked with dA in a variety of sequence contexts, but in contrast to AP and common exogenous electrophiles, reaction was not observed with dG [17–19]. In addition to forming a cross-link with dA ( 3 , Figure 2) whose structure was analogous to 2 , C4-AP reacted with dA to produce an ICL ( 4 , Figure 2) in which neither strand of the duplex was cleaved.…”