Wang Yazhen, Schnetz-Boutaud Nathalie C, Kroth Heiko, Yagi Haruhiko, Sayer Jane M, Kumar Subodh, Jerina Donald M, Stone Michael P
Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA.
Chem Res Toxicol. 2008 Jul;21(7):1348-58. doi: 10.1021/tx7004103. Epub 2008 Jun 13.
The conformation of the 1 R,2 S,3 R,4 S-benzo[ c]phenanthrene- N (2)-dG adduct, arising from trans opening of the (+)-1 S,2 R,3 R,4 S- anti-benzo[ c]phenanthrene diol epoxide, was examined in 5'- d(ATCGC XCGGCATG)-3'.5'-d(CATGCCG CGCGAT)-3', where X = 1 R,2 S,3 R,4 S-B[ c]P- N (2)-dG. This duplex, derived from the hisD3052 frameshift tester strain of Salmonella typhimurium, contains a (CG) 3 iterated repeat, a hotspot for frameshift mutagenesis. NMR experiments showed a disconnection in sequential NOE connectivity between X (4) and C (5), and in the complementary strand, they showed another disconnection between G (18) and C (19). In the imino region of the (1)H NMR spectrum, a resonance was observed at the adducted base pair X (4) x C (19). The X (4) N1H and G (18) N1H resonances shifted upfield as compared to the other guanine imino proton resonances. NOEs were observed between X (4) N1H and C (19) N (4)H and between C (5) N (4)H and G (18) N1H, indicating that base pairs X (4) x C (19) and C (5) x G (18) maintained Watson-Crick hydrogen bonding. No NOE connectivity was observed between X (4) and G (18) in the imino region of the spectrum. Chemical shift perturbations of greater than 0.1 ppm were localized at nucleotides X (4) and C (5) in the modified strand and G (18) and C (19) in the complementary strand. A total of 13 NOEs between the protons of the 1 R-B[ c]Ph moiety and the DNA were observed between B[ c]Ph and major groove aromatic or amine protons at base pairs X (4) x C (19) and 3'-neighbor C (5) x G (18). Structural refinement was achieved using molecular dynamics calculations restrained by interproton distances and torsion angle restraints obtained from NMR data. The B[ c]Ph moiety intercalated on the 3'-face of the X (4) x C (19) base pair such that the terminal ring of 1 R-B[ c]Ph threaded the duplex and faced into the major groove. The torsion angle alpha' [X (4)]-N3-C2-N2-B[ c]Ph]-C1 was calculated to be -177 degrees, maintaining an orientation in which the X (4) exocyclic amine remained in plane with the purine. The torsion angle beta' [X (4)]-C2-N2-[B[ c]Ph]-C1-C2 was calculated to be 75 degrees. This value governed the 3'-orientation of the B[ c]Ph moiety with respect to X (4). The helical rise between base pairs X (4) x C (19) and C (5) x G (18) increased and resulted in unwinding of the right-handed helix. The aromatic rings of the B[ c]Ph moiety were below the Watson-Crick hydrogen-bonding face of the modified base pair X (4) x C (19). The B[c]Ph moiety was stacked above nucleotide G (18), in the complementary strand.
研究了由（+）-1S，2R，3R，4S-反式苯并[c]菲二醇环氧化物的反式开环产生的1R，2S，3R，4S-苯并[c]菲-N（2）-dG加合物在5'-d（ATCGC XCGGCATG）-3'.5'-d（CATGCCG CGCGAT）-3'中的构象，其中X = 1R，2S，3R，4S-B[c]P-N（2）-dG。该双链体衍生自鼠伤寒沙门氏菌的hisD3052移码测试菌株，包含一个（CG）3重复序列，是移码诱变的热点。核磁共振实验表明，在X（4）和C（5）之间的顺序核Overhauser效应（NOE）连接中断，在互补链中，它们显示出G（18）和C（19）之间的另一个连接中断。在（1）H NMR谱的亚氨基区域，在加合碱基对X（4）xC（19）处观察到一个共振。与其他鸟嘌呤亚氨基质子共振相比，X（4）N1H和G（18）N1H共振向高场移动。在X（4）N1H和C（19）N（4）H之间以及C（5）N（4）H和G（18）N1H之间观察到NOE，表明碱基对X（4）xC（19）和C（5）xG（18）保持沃森-克里克氢键。在谱的亚氨基区域中，未观察到X（4）和G（18）之间的NOE连接。大于0.1 ppm的化学位移扰动位于修饰链中的核苷酸X（4）和C（5）以及互补链中的G（18）和C（19）处。在1R-B[c]Ph部分的质子与DNA之间总共观察到13个NOE，在碱基对X（4）xC（19）和3'-邻位C（5）xG（18）处的B[c]Ph与大沟芳香族或胺质子之间。使用分子动力学计算实现了结构优化，该计算受从NMR数据获得的质子间距离和扭转角约束的限制。B[c]Ph部分插入到X（4）xC（19）碱基对的3'-面，使得1R-B[c]Ph的末端环穿过双链体并面向大沟。扭转角α'[X（4）]-N3-C2-N2-[B[c]Ph]-C1经计算为-177度，保持X（4）环外胺与嘌呤共面的取向。扭转角β'[X（4）]-C2-N2-[B[c]Ph]-C1-C2经计算为75度。该值决定了B[c]Ph部分相对于X（4）的3'-取向。碱基对X（4）xC（（19）和C（5）xG（18）之间的螺旋上升增加，导致右手螺旋解旋。B[c]Ph部分的芳香环位于修饰碱基对X（4）xC（19）的沃森-克里克氢键面下方。B[c]Ph部分堆叠在互补链中的核苷酸G（18）上方。
