Li Z, Mao H, Kim H Y, Tamura P J, Harris C M, Harris T M, Stone M P
Department of Chemistry, Center in Molecular Toxicology, Vanderbilt University, Nashville, Tennessee 37235, USA.
Biochemistry. 1999 Mar 9;38(10):2969-81. doi: 10.1021/bi982072x.
The solution structure of the (-)-(1R,2S,3R,4S)-N6-[1-(1,2,3, 4-tetrahydroxy-benz[a]anthracenyl)]-2'-deoxyadenosyl adduct at X6 of 5'-d(CGGACXAGAAG)-3'.5'-d(CTTCTTGTCCG)-3', incorporating codons 60, 61(italic), and 62 of the human N-ras protooncogene, was determined. This adduct results from the trans opening of 1S,2R,3R,4S-1, 2-epoxy-1,2,3,4-tetrahydro-benz[a]anthracenyl-3,4-diol by the exocyclic N6 of adenine. Molecular dynamics simulations were restrained by 509 NOEs from 1H NMR. The precision of the refined structures was monitored by pairwise root-mean-square deviations which were <1.2 A; accuracy was measured by complete relaxation matrix calculations, which yielded a sixth root R factor of 9.1 x 10(-)2 at 250 ms. The refined structure was a right-handed duplex, in which the benz[a]anthracene moiety intercalated from the major groove between C5.G18 and R,S,R,SA6.T17. In this orientation, the saturated ring of BA was oriented in the major groove of the duplex, with the aromatic rings inserted into the duplex such that the terminal ring of BA threaded the duplex and faced toward the minor groove direction. The duplex suffered localized distortion at and immediately adjacent to the adduct site, evidenced by the increased rise of 8.8 A as compared to the value of 3.5 A normally observed for B-DNA between base pairs C5.G18 and R,S,R,SA6.T17. These two base pairs also buckled in opposite directions away from the intercalated BA moiety. The refined structure was similar to the (-)-(7S,8R,9S,10R)-N6-[10-(7,8,9, 10)-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct of corresponding stereochemistry at X6 of the same oligodeoxynucleotide [Zegar, I. S., Kim, S. J., Johansen, T. N., Horton, P. J., Harris, C. M., Harris, T. M., and Stone, M. P. (1996) Biochemistry 35, 6212-6224]. Both adducts intercalated toward the 5'-direction from the site of adduction. The similarities in solution structures were reflected in similar biological responses, when repair-deficient AB2480 Escherichia coli were transformed with M13mp7L2 DNA site-specifically modified with these two adducts.
测定了5'-d(CGGACXAGAAG)-3'.5'-d(CTTCTTGTCCG)-3'中X6位点处(-)-(1R,2S,3R,4S)-N6-[1-(1,2,3,4-四羟基-苯并[a]蒽基)]-2'-脱氧腺苷加合物的溶液结构，该序列包含人N-ras原癌基因的密码子60、61（斜体）和62。此加合物是由腺嘌呤的外环N6对1S,2R,3R,4S-1,2-环氧-1,2,3,4-四氢-苯并[a]蒽基-3,4-二醇进行反式开环反应形成的。分子动力学模拟由1H NMR的509个核Overhauser效应（NOE）约束。通过成对均方根偏差监测精修结构的精度，该偏差<1.2 Å；通过完全弛豫矩阵计算测量准确性，在250 ms时得到的六次方根R因子为9.1×10⁻²。精修结构为右手双链体，其中苯并[a]蒽部分从C5.G18和R,S,R,SA6.T17之间的大沟插入。在此方向上，BA的饱和环位于双链体的大沟中，芳香环插入双链体，使得BA的末端环穿过双链体并朝向小沟方向。与B-DNA中碱基对C5.G18和R,S,R,SA6.T17之间通常观察到的3.5 Å值相比，加合物位点及其紧邻区域的双链体出现局部扭曲，表现为上升增加了8.8 Å。这两个碱基对也朝着远离插入的BA部分的相反方向弯曲。精修结构与相同寡脱氧核苷酸X6位点处具有相应立体化学的(-)-(7S,8R,9S,10R)-N6-[10-(7,8,9,10)-四氢苯并[a]芘基)]-2'-脱氧腺苷加合物相似[泽加尔，I. S.，金，S. J.，约翰森，T. N.，霍顿，P. J.，哈里斯，C. M.，哈里斯，T. M.，和斯通，M. P.（1996年）《生物化学》35卷，6212 - 6224页]。两种加合物均从加合位点向5'-方向插入。当用这两种加合物进行位点特异性修饰的M13mp7L2 DNA转化修复缺陷型AB2480大肠杆菌时，溶液结构的相似性反映在相似的生物学反应中。
