Single C8-Arylguanine Modifications Render Oligonucleotides in the Z-DNA Conformation under Physiological Conditions

Abstract

Z-DNA is the only DNA conformation that has a left-handed helical twist. Although Z-DNA has been implicated in both carcinogenesis and mutagenesis, its specific biological role remains uncertain. We have demonstrated that the formation of C8-arylguanine DNA adducts, derived from arylhydrazines, shifts the B/Z-DNA equilibrium toward the Z-DNA conformation in d(CG)5 sequences. However, our previous work examined the effect of two adducts in the duplex, and it was unclear whether the two base modifications were working together to cause the equilibrium shift toward the Z-DNA conformation. Here we report the synthesis and characterization of a hairpin oligonucleotide sequence (d(CG)5T4(CG)5) containing only one C8-arylguanine modified base. The unmodified hairpin and the previously studied unmodified double-stranded oligonucleotide were conformationally similar, and each required ∼3 M NaCl to yield a B-/Z-DNA ratio of 1:1. The introduction of a single C8-arylguanine modification significantly reduced the NaCl concentration needed to produce a 1:1 B-/Z-DNA ratio in the hairpin. Further, the addition of MgCl2 and spermine to the C8-arylguanine-modified hairpin shifts the B/Z-DNA equilibrium such that the Z form predominated under physiological conditions. NMR and molecular modeling indicated the conformational effects produced by the C8-arylguanine modification occurred locally at the site of modification while CD data demonstrated that the C8-arylguanine-modified base destabilized the B form. Additionally, our data show that adopting the Z-DNA conformation is preferred over denaturation to the single-stranded form. Finally, the conformational effects of the C8-arylguanine modifications were not additive and the introduction of any such modifications drive Z-DNA formation under physiological conditions, which may provide a novel carcinogenesis mechanism where DNA adducts confer their carcinogenicity through a Z-DNA-mediated mechanism.

Structural and biochemical impact of C8-aryl-guanine adducts within the NarI recognition DNA sequence: influence of aryl ring size on targeted and semi-targeted mutagenicity

“…The resulting N-linked C8-dG adducts contain a flexible amine tether separating the dG component from the aryl ring and there is a strong established relationship between the resulting conformational heterogeneity and biological effects ( 5 , 6 ). The structurally related aromatic organic carcinogens, such as polycyclic aromatic hydrocarbons (PAHs) ( 7 – 9 ), arylhydrazines ( 10 – 12 ) and phenols ( 13 – 16 ), may also undergo bioactivation, producing aryl radical species that covalently attach to the C8-site of dG to produce carbon-linked C8-aryl-dG adducts. In these cases, the adducts are similar in structure to their N-linked counterparts in terms of aryl ring size and shape, but do not have an amine linkage, thereby altering the orientation of the modification in the DNA duplex as well as reducing conformational flexibility.…”

“…For example, the PAH benzo[a]pyrene (B[a]P) undergoes peroxidase-mediated oxidation to afford radical cations ( 7 , 8 ), where the potential involvement of the C8-B[a]P-dG lesion produces G → T and G → C transversion mutations in yeast ( 9 ). Additionally, arylhydrazines generate phenyl radicals, produce C8-phenyl-dG adducts ( 10 – 12 ) and are mutagenic in bacteria ( 35 ). Finally, the chlorophenolic mycotoxin ochratoxin A (OTA) gives rise to a C-linked C8-aryl-dG adduct in vivo ( 14 , 15 ) and deletion mutations have been observed in the kidney tissue of male rats exposed to OTA ( 36 – 38 ).…”

“…Among these adducts, PhG is a known adduct derived from the carcinogen phenylhydrazine ( vide supra ). CNPhG is a mimic for adducts arising from para -substituted aryl hydrazines, such as para -CH 3 -PhG, para -HOOC-PhG and para -H 3 COC-PhG ( 10 – 12 ). QG is a mimic for a portion of PAH lesions (e.g.…”

Lanthanum induced B-to-Z transition in self-assembled Y-shaped branched DNA structure

“…This view has been changed gradually over the past 30 years. Now it is known that CA and AT repeats as well as some heterogenous sequences can readily form Z-DNA in the presence of salts or metal complexes19202122232425. Recently, the B-Z transition has been explored from nanotechnological points of view and used as the driving machinery of many nanomechanical devices262728.…”

C‐C Bond Formation: Synthesis of C5 Substituted Pyrimidine and C8 Substituted Purine Nucleosides Using Water Soluble Pd‐imidate Complex

“…Found: C,58.73;H,4.71;N,18.96. 8-(4-Methylphenyl)-2 -deoxyguanosine (S.12a): (Train et al, 2014) white solid, yield 78%. 1 H NMR (500 MHz, DMSO-d 6 ) δ 10.75 (s,1 H),7.52 (d,J = 7.5 Hz,2 H),7.33 (d,J = 7.5 Hz,2 H),6.39 (s,2 H),6.04 (t,J = 7.0 Hz,1 H),5.14 (d,J = 3.1 Hz,1 H),4.99 (d,J = 4.6 Hz, 1 H), 4.32 (s, 1 H), 3.77 (s, 1 H), 3.57 (ddd,J = 21.6,11.2,5.8 Hz,2 H),2.37 (s,3 H),1.99 (dd,J = 11.5,5.6 Hz,1 H).…”