Solution conformation of the (+)-trans-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the major groove.
This paper reports on the solution structure of the (+)-trans-anti-[BP]dG adduct positioned opposite a deletion site in a DNA oligomer duplex which defines the alignment of this covalent benzo[a]pyrene-N2-deoxyguanosine stereosiomer relative to the deletion site. The combined NMR-molecular mechanics computation studies were undertaken on the (+)-trans-anti-[BP]dG adduct embedded in the d(C5-[BP]G6-C7).d(G16-G17) sequence context in a duplex containing 11 residues on the modified strand and 10 on the partner, with no base opposite the modification. The exchangeable and nonexchangeable protons of the benzo[a]pyrenyl moiety and the nucleic acid were assigned following analysis of two-dimensional NMR data sets in H2O and D2O solution. The solution conformation of the (+)-trans-anti-[BP]dG.del 11-mer duplex has been determined by incorporating intramolecular and intermolecular proton-proton distances defined by lower and upper bounds deduced from NOESY spectra as restraints in molecular mechanics computations in torsion angle space. The benzo[a]pyrene ring of [BP]dG6 is intercalated between intact Watson-Crick dC5.dG17 and dC7.dG16 base pairs with the deoxyguanosine base of [BP]dG6 displaced into the major groove. The intercalation site is wedge shaped, being narrower toward the dG16-dG17 step on the deletion-containing strand. The deoxyguanosine base of [BP]dG6 which is positioned in the major groove is inclined relative to the helix axis and stacks over the 5'-flanking dC5 residue in the solution structure. The intercalative-base displacement structure of the (+)-trans-anti-[BP]dG.del 11-mer duplex exhibits several unusually shifted proton resonances which can be readily accounted for by the ring current contribution of the deoxyguanosyl and pyrenyl rings of the [BP]dG6 adduct. This solution structure of the (+)-trans-anti-[BP]dG.del 11-mer duplex where the pyrene ring intercalates into the helix with displacement of the modified deoxyguanosine into the major groove strikingly contrasts with our previous study on the (+)-trans-anti-[BP]dG.dC 11-mer duplex [Cosman, M., et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1914-1918] where the benzo[a]pyrene ring is positioned in the minor groove without disruption of the Watson-Crick pairing at the [BP]dG.dC modification site. Thus, generation of the deletion site following removal of the dC opposite the (+)-trans-anti-[BP]dG results in a displacement of the entire [BP]dG residue toward the major groove and intercalation of the benzo[a]pyrene ring into the helix.
Cosman
M
M
Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021.
Fiala
R
R
Hingerty
B E
BE
Amin
S
S
Geacintov
N E
NE
Broyde
S
S
Patel
D J
DJ
D001483:Base Sequence; D001564:Benzo(a)pyrene / Q000737:chemistry*; D002274:Carcinogens, Environmental / Q000737:chemistry*; D018736:DNA Adducts / Q000737:chemistry*; D003849:Deoxyguanosine / Q000031:analogs & derivatives*; D007364:Intercalating Agents / Q000737:chemistry*; D007536:Isomerism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011522:Protons; D017384:Sequence Deletion; D012996:Solutions
D002274:Carcinogens, Environmental; D018736:DNA Adducts; D007364:Intercalating Agents; D011522:Protons; D012996:Solutions; C056612:benzo(a)pyrene-DNA adduct; D001564:Benzo(a)pyrene; D003849:Deoxyguanosine