Styrene Oxide Adducts in an Oligodeoxynucleotide Containing the Human N-ras Codon 12:  Minor Groove Structures of the R(12,1)- and S(12,1)-α-(N²-Guanyl) Stereoisomers Determined by ¹H Nuclear Magnetic Resonance

Abstract

The R- and S-alpha-(N2-guanyl)styrene oxide (SO) adducts at X5 in d(G1G2C3A4X5G6T7G8G9T10G11).d(C12A13C14C15A16C17C18T19G20C21C22 ), encompassing codon 12 of the human N-ras protooncogene (underlined), were examined using 1H NMR spectroscopy. These were the R(12,1) and S(12,1) adducts, indicating the location of the R or S adduct at the first position of codon 12. These differed from the R- and S(12, 2)-alpha-SO adducts [Zegar, I. S., Setayesh, F. R., DeCorte, B. L., Harris, C. M., Harris, T. M., and Stone, M. P. (1996) Biochemistry 35, 4334-4348] in that the base pair 5' to the lesion was changed from G.C to A.T, while the base pair 3' to the lesion was changed from T.A to G.C. Comparison of the R- and S(12,1) adducts with the R- and S(12,2) adducts allowed the effects of flanking bases on the conformations of the alpha-SO adducts to be examined. This change in flanking base affected the R-SO lesion. The R(12,1) adduct structure was disordered at the adduct site, and a refined structure could not be obtained. NOE and chemical shift data suggested that the styrenyl moiety was oriented in the minor groove and in the 3'-direction from the site of adduction. In contrast, this change in flanking base did not affect the S-SO lesion. The S(12,1) adduct yielded a refined structure, with the styrenyl moiety edgewise in the minor groove and oriented in the 5'-direction relative to the site of adduction. A total of 232 interproton distances, including 13 styrene-DNA distances, were obtained. A total of 12 NOE-restrained molecular dynamics calculations converged with pairwise root-mean-square deviation of 1.10 A. The sixth-root residual index between calculated and experimental NOE intensities was 8.0 x 10(-)2 A. The styrene aromatic protons appeared as three resonances, suggesting rapid rotation. The possibility of a hydrogen bond between the styrene hydroxyl and C18 O2 in the S(12,1) adduct could not be confirmed. This work illustrates the dual roles of stereochemistry and sequence in modulating the properties of guanine N2 alpha-SO adducts.

NMR Structures of Damaged DNA

“…The structure of DNA duplexes having an S ( 133a ) or R ( 133b ) α-styrene oxide- N 2 -dG adduct ((α-SO- N 2 -dG) paired to dC has been described. , As compared to previous PAH lesions, α-SO- N 2 -dG adducts (Chart ) have a single benzyl group attached to the guanine amino nitrogen, reducing minor-groove crowding at the lesion site. The NMR-refined models establish the presence of right-handed helical structures with all residues in the anti range around the χ torsion angle and WC base pair alignments throughout the duplex, including at the lesion containing base pair.…”

Repair-Resistant DNA Lesions

“…71 Additional results have been published since then. 77−80 Other significant contributions to our understanding of the structures of PAH-derived DNA adducts include those from the Stone laboratory 81−89 as well as by Jerina and collaborators. 90−94 Other types of bulky DNA adducts that have been structurally characterized include those derived from 2-aminofluorenes (AF) and N -acetylaminofluorene (AAF), 95−103 2-aminopyrene, 104 fluorene-labeled AF and AAF, 105−108 heterocyclic aromatic amines, 109−112 and other bulky and nonbulky DNA lesions described below.…”

“…The structural features of a variety of stereochemically and structurally distinct PAH diol epoxide-derived DNA adducts have been reviewed . Additional results have been published since then. − Other significant contributions to our understanding of the structures of PAH-derived DNA adducts include those from the Stone laboratory − as well as by Jerina and collaborators. − Other types of bulky DNA adducts that have been structurally characterized include those derived from 2-aminofluorenes (AF) and N -acetylaminofluorene (AAF), − 2-aminopyrene, fluorene-labeled AF and AAF, − heterocyclic aromatic amines, − and other bulky and nonbulky DNA lesions described below. , Collectively, these publications represent a rich source of information on the conformational features of structurally diverse forms of bulky DNA adducts for studying the relationships between their properties and their impact on biological phenomena…”

Influence of the Linkage Type and Functional Groups in the Carcinogenic Moiety on the Conformational Preferences of Damaged DNA: Structural and Energetic Characterization of Carbon- and Oxygen-Linked C8-Phenolic-Guanine Adducts

“…To the best of our knowledge, no other previously studied C 8 -dG adduct involves a more extended linker than the PhO dG adduct. However, the previously studied N-linked N 2 -dG styrene oxide adducts 53,54 contain a −NH−CH 2 − linkage, which leads to an extrahelical (minor) groove DNA structure. Unfortunately, these are minor groove adducts and therefore difficult to compare to the phenolic adducts considered in the present study.…”