DNA Sequence Modulates the Conformation of the Food Mutagen 2-Amino-3-methylimidazo[4,5-f]quinoline in the Recognition Sequence of the NarI Restriction Enzyme^,

Abstract

The conformations of C8-dG adducts of 2-amino-3-methylimidazo [4,5-f]quinoline (IQ) positioned in the C-X 1 -G, G-X 2 -C, and C-X 3 -C contexts in the C-G 1 -G 2 -C-G 3 -C-C recognition sequence of the NarI restriction enzyme were compared, using the oligodeoxynucleotides 5′- d (CTCXGCGCCATC)-3′·5′-d(GATGGCGCCGAG)-3′, 5′-d(CTCGXCGCCATC)-3′·5′-d (GATGGCGCCGAG)-3′, and 5′-d(CTCGGCXCCATC)-3′·5′-d(GATGGCGCCGAG)-3′ (X is the C8-dG adduct of IQ). These were the NarIIQ1, NarIIQ2, and NarIIQ3 duplexes, respectively. In each instance, the glycosyl torsion angle χ for the IQ-modified dG was in the syn conformation. The orientations of the IQ moieties were dependent upon the conformations of torsion angles α′ [N9-C8- N(IQ)-C2(IQ)] and β′ [C8-N(IQ)-C2(IQ)-N3(IQ)], which were monitored by the patterns of 1 H NOEs between the IQ moieties and the DNA in the three sequence contexts. The conformational states of IQ torsion angles α′ and β′ were predicted from the refined structures of the three adducts obtained from restrained molecular dynamics calculations, utilizing simulated annealing protocols. For the NarIIQ1 and NarIIQ2 duplexes, the α′ torsion angles were predicted to be −176 ± 8° and −160 ± 8°, respectively, whereas for the NarIIQ3 duplex, torsion angle α′ was predicted to be 159 ± 7°. Likewise, for the NarIIQ1 and NarIIQ2 duplexes, the β′ torsion angles were predicted to be −152 ± 8° and −164 ± 7°, respectively, whereas for the NarIIQ3 duplex, torsion angle β′ was predicted to be −23 ± 8°. Consequently, the conformations of the IQ adduct in the NarIIQ1 and NarIIQ2 duplexes were similar, with the IQ methyl protons and IQ H4 and H5 protons facing outward in the minor groove, whereas in the NarIIQ3 duplex, the IQ methyl protons and the IQ H4 and H5 protons faced into the DNA duplex, facilitating the base-displaced intercalated orientation of the IQ moiety [Wang, F., Elmquist, C. E., Stover, J. S., Rizzo, C. J., and Stone, M. P. (2006) J. Am. Chem. Soc. 128, 10085 † This work was supported by NIH Grant CA-55678 (M.P.S.). The Vanderbilt Center for Molecular Toxicology is funded by a center grant from the National Institute of Environmental Health Sciences (NIEHS) (ES-00267). J.S.S. was supported by NIEHS Predoctoral Traineeship ES-07028. Funding for the NMR spectrometers was supplied in part by NIH Grant RR-05805, the Vanderbilt Center in Molecular Toxicology, and Vanderbilt University. The Vanderbilt-Ingram Cancer Center is funded by a center grant from the National Center Institute (NCI) (CA-68485). ‡ The PDB ID code for the NarIIQ1 duplex structure is 2Z2G and the PDB ID code for the NarIIQ2 duplex structure is 2Z2H.© 2007 American Chemical Society * To whom correspondence should be addressed. C.J.R.: telephone, (615) 322−6100; fax, (615) 343−1234; e-mail, c.rizzo@vanderbilt.edu. M.P.S.: telephone, (615) 322−2589; fax, (615) 322−7591; e-mail, michael.p.stone@vanderbilt.edu.. SUPPORTING INFORMATION AVAILABLE Nonexchangeable proton chemical shifts of the modified NarIIQ1 and NarIIQ2 duplexes (Table S1), exchangeabl...

Synthesis of Oligonucleotides Containing the N2-Deoxyguanosine Adduct of the Dietary Carcinogen 2-Amino-3-methylimidazo[4,5-f]quinoline

“…We were able to make preliminary conformational assignments for the dGuo-C8-IQ adducts based on UV absorption and CD spectroscopy, and these predictions were subsequently confirmed by a full structural analysis by a combination of high-field NMR and restrained molecular dynamics (31,78,79). The conformation of dGuo-N 2 -PAH adducts was also correlated to their UV spectra (85).…”

Repair-Resistant DNA Lesions

“…111,112 All three 12-mer duplexes are destabilized by these adducts with Δ T m in the range of −4 to −7 °C. 110 …”

Structural and energetic characterization of the major DNA adduct formed from the food mutagen ochratoxin A in the NarI hotspot sequence: influence of adduct ionization on the conformational preferences and implications for the NER propensity

“…Since OTA exposure has been linked to an increase in the frequency of deletion mutations at carcinogenic target sites ( 20 , 26 ), we chose the Nar I sequence to study the conformational preferences of the OTB-dG lesion. This choice also allows direct comparison of the conformational preferences of the OTB-dG adduct with widely studied C8-bonded N-linked carcinogenic aromatic amine lesions ( 41 , 49 , 51 – 54 ), and thereby the elucidation of the role of adduct structure in dictating the DNA conformational preferences. Our results indicate that OTB-dG adducted DNA has the tendency to adopt a mixture of major groove, wedge and base-displaced intercalated conformations when paired against complementary cytosine in the Nar I sequence.…”