Kozack R E, Loechler E L
Department of Biology, Boston University, MA 02215, USA.
Carcinogenesis. 1999 Jan;20(1):85-94. doi: 10.1093/carcin/20.1.85.
The potent mutagen/carcinogen 7R,8S-dihydroxy-9S, 10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-anti-B[a]PDE], which is the activated form of benzo[a]pyrene (B[a]P), is able to induce different kinds of mutations (G-->T, G-->A, etc.). One hypothesis for this is that different mutations are induced depending upon the conformation of its major adduct ([+ta]-B[a]P-N2-dG) when bypassed during DNA replication. Based on molecular modeling, there appear to be at least 16 potential conformations that the major adduct [+ta]-B[a]P-N2-dG can adopt in dsDNA. Regarding base substitution mutagenesis, eight conformations are most likely to be relevant. In two conformations the dG moiety of the adduct is base paired with its complementary dC and the B[a]P moiety is in the minor groove. In two others the dG moiety of the adduct is in the Hoogsteen orientation and the B[a]P moiety is in the major groove. There are four base displaced structures in which the B[a]P moiety of the adduct is stacked with the surrounding base pairs, two with dG in the major groove and two with dG in the minor groove. Using a simulated annealing protocol, these eight conformations were evaluated in five different DNA sequence contexts (5'-TGC-3', 5'-CGT-3', 5'-AGA-3', 5'-CGG-3' and 5'-GGG-3'); the latter were chosen because they may be particularly revealing about mutagenic mechanism based on studies with [+ta]-B[a]P-N2-dG and (+)-anti-B[a]PDE. For each conformation and each sequence context, 25 simulated annealing runs were conducted by systematically varying several parameters (such as the initial annealing temperature) based on a protocol established recently. The goal of this work was to exclude conformations that are clearly inferior. Three conformations are virtually always high in energy, including the two Hoogsteen oriented species and one of the base displaced species with dG in the major groove. Remarkably, the remaining five conformations are often quite close in energy and are deemed most likely to be relevant to mutagenesis (see accompanying paper).
强效诱变剂/致癌物7R,8S-二羟基-9S,10R-环氧-7,8,9,10-四氢苯并[a]芘[(+)-反式-B[a]PDE]是苯并[a]芘（B[a]P）的活化形式，能够诱导不同类型的突变（G→T、G→A等）。对此的一种假说是，在DNA复制过程中绕过其主要加合物（[+ta]-B[a]P-N2-dG）时，会根据其构象诱导不同的突变。基于分子建模，主要加合物[+ta]-B[a]P-N2-dG在双链DNA中似乎可以采取至少16种潜在构象。关于碱基置换诱变，八种构象最有可能相关。在两种构象中，加合物的dG部分与其互补的dC碱基配对，而B[a]P部分位于小沟中。在另外两种构象中，加合物的dG部分处于Hoogsteen取向，而B[a]P部分位于大沟中。有四种碱基移位结构，其中加合物的B[a]P部分与周围的碱基对堆积，两种结构中dG在大沟中，两种结构中dG在小沟中。使用模拟退火协议，在五种不同的DNA序列背景（5'-TGC-3'、5'-CGT-3'、5'-AGA-3'、5'-CGG-3'和5'-GGG-3'）中对这八种构象进行了评估；选择后者是因为基于对[+ta]-B[a]P-N2-dG和(+)-反式-B[a]PDE的研究，它们可能对诱变机制有特别的揭示作用。对于每种构象和每种序列背景，根据最近建立的协议系统地改变几个参数（如初始退火温度）进行了25次模拟退火运行。这项工作的目标是排除明显较差的构象。三种构象实际上能量总是很高，包括两种Hoogsteen取向的物种和一种大沟中dG的碱基移位物种。值得注意的是，其余五种构象的能量通常非常接近，被认为最有可能与诱变有关（见随附论文）。
