Wobble dC·dA Pairing 5‘ to the Cationic Guanine N7 8,9-Dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B₁ Adduct:  Implications for Nontargeted AFB₁ Mutagenesis

Abstract

The structure of 5'-d(ACATC(AFB)GATCT)-3'.5'-d(AGATCAATGT)-3', containing the C(5).A(16) mismatch at the base pair 5' to the modified (AFB)G(6), was determined by NMR. The characteristic 5'-intercalation of the AFB(1) moiety was maintained. The mismatched C(5).A(16) pair existed in the wobble conformation, with the C(5) imino nitrogen hydrogen bonded to the A(16) exocyclic amino group. The wobble pair existed as a mixture of protonated and nonprotonated species. The pK(a) for protonation at the A(16) imino nitrogen was similar to that of the C(5).A(16) wobble pair in the corresponding duplex not adducted with AFB(1). Overall, the presence of AFB(1) did not interfere with wobble pair formation at the mismatched site. Molecular dynamics calculations restrained by distances derived from NOE data and torsion angles derived from (1)H (3)J couplings were carried out for both the protonated and nonprotonated wobble pairs at C(5).A(16). Both sets of calculations predicted the A(16) amino group was within 3 A of the C(5) imino nitrogen. The calculations suggested that protonation of the C(5).A(16) wobble pair should shift C(5) toward the major groove and shift A(16) toward the minor groove. The NMR data showed evidence for the presence of a minor conformation characterized by unusual NOEs between T(4) and (AFB)G(6). T(4) is two nucleotides in the 5'-direction from the modified base. These NOEs suggested that in the minor conformation nucleotide T(4) was in closer proximity to (AFB)G(6) than would be expected for duplex DNA. Modeling studies examined the possibility that T(4) transiently paired with the mismatched A(16), allowing it to come within NOE distance of (AFB)G(6). This model structure was consistent with the unusual NOEs associated with the minor conformation. The structural studies are discussed in relationship to nontargeted C --> T transitions observed 5' to the modified (AFB)G in site-specific mutagenesis experiments [Bailey, E. A., Iyer, R. S., Stone, M. P., Harris, T. M., and Essigmann, J. M. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 1535-1539].

Genetic Single Nucleotide Polymorphisms (GSNPs) in the DNA Repair Genes and Hepatocellular Carcinoma Related to Aflatoxin B1 among Guangxiese Population

“…For AFB1-DNA adducts, AFB1-N 7 -Gua adduct, the most common adduct type, is primarily identiied and conirmed in vivo research studies [17][18][19][20][21][22], whereas the formamidopyridine AFB1 adduct (AFB1-FAPy) is a ring-opened DNA adduct [23,24]. Because of the accumulations of AFB1-FAPy, it is characterized by a time-dependent and non-enzyme way and exhibits apparent persistence in DNA; it may be of biological basis of genes mutation.…”

DNA Repair Capacity-Related to Genetic Polymorphisms of DNA Repair Genes and Aflatoxin B1-Related Hepatocellular Carcinoma Among Chinese Population

“…Therefore, AFB1 has been classified as a category I known human carcinogen by the International Agency for Research on Cancer (24). AFB1 is metabolized by cytochrome P450 enzymes to its reactive form, AFB1-8,9-epoxide (AFB1-epoxide), which covalently binds to DNA and induces DNA damage (19,(25)(26)(27)(28). DNA damage induced by AFB1 includes AFB1-DNA adducts, oxidative DNA damage, www.intechopen.com and gene mutation (Fig.…”

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

“…11 Wobble A + •C base pairs may also form in DNA under biologically relevant conditions, 12 where they can have mutagenic and carcinogenic effects. 13,14 Apart from these structural influences, it has been suggested that the elevated pKa of these nucleic acids may play a significant role in ribozyme catalysis, as these protonated residues may be involved in general acid-base catalysis, playing an analogous role to histidine residues in proteins. 15-19 Some examples of its role in catalysis include hepatitis delta virus ribozyme 20-24 and hairpin ribozyme, 25-30 where experimental studies have demonstrated that a loss-of-function mutation of key residues that have elevated pKa values led to a significant drop in catalytic activity.…”