Prev. Article Next Article Table of Contents

Article

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^†^,^‡

Supporting Info

Feng Wang, C. Eric Elmquist, James S. Stover, Carmelo J. Rizzo,* and Michael P. Stone*

Department of Chemistry, Center in Molecular Toxicology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235

Biochemistry, 2007, 46 (29), pp 8498–8516

DOI: 10.1021/bi700361u

Publication Date (Web): June 30, 2007

†

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.

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.

Abstract

The conformations of C8-dG adducts of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) positioned in the C-X¹-G, G-X²-C, and C-X³-C contexts in the C-G¹-G²-C-G³-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 ¹H 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, 10085−10095]. In contrast, for the NarIIQ1 and NarIIQ2 duplexes, the IQ moiety remained in the minor groove. These sequence-dependent differences suggest that base-displaced intercalation of the IQ adduct is favored when both the 5‘- and 3‘-flanking nucleotides in the complementary strand are guanines. These conformational differences may correlate with sequence-dependent differences in translesion replication.