Adduct conformation

On the basis of PAH physical binding studies (18) it has been previously suggested that BPDE adduct conformations are strongly dependent upon the DNA environment and that this may be playing a role in the varying results reported by different laboratories. A mechanism for reaction has been proposed (2) which involves initial intercalation of BPDE followed by reaction which can lead ultimately to nonintercalated complexes. This mechanism is supported by recent kinetic flow dichroism studies (69). 

Kozack R, Seo KY, Jelinsky SA, et al. Toward an understanding of the role of DNA adduct conformation in defining mutagenic mechanism based on studies of the major adduct (formed at N2-dG) of the potent environmental carcinogen benzo[a]pyrene. Mutat Res 2000 450(1-2) 41-59. 

In our opinion, the most satisfactory conclusion from the NMR-based modeling work is that there is essentially one conformer regardless of sequence. We believe this conformer has features which have not been found in other DNA s and which cannot be easily modeled. Therefore, numerous related models have been proposed to fit the data obtained for different PtD duplexes under various experimental conditions. Thus, additional efforts to define the relationship between NMR-spectral features and adduct conformation are needed. 

Due to the steric demands of the phenylthio group in conformer 100, the aldehyde preferentially attacks the top face of the enolate giving an awft-Michael adduct, while with conformer 101 the aldehyde comes from the bottom face to give a syw-Michael adduct. Conformer 100 should be the more favorable, due to the steric repulsion between the methyl group and the oxygen atom in the enolate unit (Scheme 35). 

Dependence of Nucleotide Excision Repair by E. coli UvrABC Proteins on Adduct Conformation... 

Extensive studies by NMR methods have shown that the conformations of PAH diol epoxide-N2-dG and - N6-dA adducts in double-stranded DNA depend markedly on the stereochemistry, PAH topology, and base sequence context Earlier work has been summarized by us [53]. Since then, we have published the NMR solution structures of a number of other DNA adducts [79, 88, 89, 92]. The structural properties of various DNA adducts have been reviewed more recently by Lukin and de los Santos [93]. The basic structural motifs, based on our work and that of others [94—98] that are relevant to the NER studies described in this chapter, are summarized in Figure 12.3. Computational analyses have provided insights into the origins and stereochemistry dependence of these remarkably different adduct conformations [26, 42, 47, 54, 99]. In the following, we summarize the main features of these different conformations. 

Sequence/adduct Conformation Prominent Watson-Crick hydrogen-bonding disturbance Bend Minor groove width... 

Alekseyev, Y.O. and Romano, LJ. (2002) Effects of benzo[a]pyrene adduct stereochemistry on downstream DNA replication in vitro evidence for different adduct conformations within the active site of DNA polymerase I (Klenow fragment). Biochemistry, 41, 4467-4479. 

Seo, K.-Y., Nagalingam, A., and Loechler, E.L. (2005) Mutagenesis studies on four stereoisomeric N -dG benzo[a]pyrene adducts in the identical 5 -CGC sequence used in NMR studies although adduct conformation differs, mutagenesis outcome does not as G -> T mutations dominate... 

Adducts ability to bind to DNA and persist to form mutations is dependent on the adduct conformation inside the DNA sequence and of the identifieation of the lesion by the repair system (Wu et al., 2002). Formation of the PAH-DNA adduets ean lead to a induction of mutations, which activate the protoongenes ras) or inaetivate the tumor suppressor genes (p53) that can trigger the tiunorization initiation process (Prahalad et al., 1997 Straif et al., 2005). 

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