Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis.
Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis.
复制标题
大体积致癌物-DNA 加合物诱导弯曲的碱基序列效应：实验和计算分析。
DOI：
10.1021/bi002643x
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发表时间：
2001
期刊：
影响因子：
2.9
通讯作者：
Geacintov,NE
中科院分区：
文献类型：
--
作者：
Ruan,Q;Zhuang,P;Li,S;Perlow,R;Srinivasan,AR;Lu,XJ;Broyde,S;Olson,WK;Geacintov,NE
大量诱变或致癌化合物与DNA的共价结合可导致弯曲，这可能显著改变DNA与关键复制和转录蛋白的相互作用。由于(+)- 7r,8S,9S， 10r -抗BPDE对映体在啮齿类动物中具有高度致瘤性，而(-)- 7s,8R,9R， 10s -抗BPDE对映体则不具有致瘤性，因此，从高活性海湾区(+)-和(−)-抗BPDE对映体衍生的加合物的影响引起了人们的兴趣。（+）-和(−)-抗bpde主要通过鸟嘌呤外环氨基的转加成与DNA共价结合，生成10S(+)-和10R(−)-反式抗-[BP]- n2 - dg加合物。我们在碱基序列上下文XG*Y中合成了许多不同的具有单(+)-和(−)-反-[BP]- n2 - dg加合物（G*）的寡核苷酸，其中X和Y是不同的DNA碱基。G*残基位于11个碱基对（~ 1个螺旋转）或16个碱基对（~ 1.5个螺旋转）双链的中心或靠近中心。除了X、Y和它们的搭档，所有的碱基都是相同的。这些序列与T4连接酶自连接形成多聚体，在天然聚丙烯酰胺凝胶中电泳产生阶梯带。每个寡核苷酸的弯曲程度是通过监测这些线性的、自连接的低聚物相对于相同碱基序列的未修饰寡核苷酸的凝胶迁移率的降低来评估的。然后使用序列特定的三维模型估计全局弯曲的程度，从中可以提取病变部位附近的碱基对步进参数roll的值。我们发现(+)-反式-[BP]- n2 - dg加合物比（−）异构体更弯曲，无论序列如何，[BP]- n2 - dg损伤部位两侧的A-T碱基对允许与加合物构象异质性一致的局部柔韧性。有趣的是，与盐水溶液相比，使用经典重复处理的计算和观察凝胶迁移率的拟合需要增强凝胶中未修饰的DNA柔韧性。两种立体异构体加合物的弯曲差异和观察到的碱基序列上下文效应可能在细胞复制、转录和修复酶对这些病变的不同处理中起重要作用。
The covalent binding of bulky mutagenic or carcinogenic compounds to DNA can lead to bending, which could significantly alter the interactions of DNA with critical replication and transcription proteins. The impact of adducts derived from the highly reactive bay region enantiomeric (+)- and (−)-anti-7,8-diol-9,10-epoxide derivatives of benzo[a]pyrene (BPDE) are of interest because the (+)-7R,8S,9S,10R-anti-BPDE enantiomer is highly tumorigenic in rodents, while the (−)-7S,8R,9R,10S-anti-BPDE enantiomer is not. Both (+)- and (−)-anti-BPDE bind covalently with DNA predominantly bytransaddition at the exocyclic amino group of guanine to yield 10S(+)- and 10R(−)-trans-anti-[BP]-N2-dG adducts. We have synthesized a number of different oligonucleotides with single (+)- and (−)-trans-anti-[BP]-N2-dG adducts (G*) in the base sequence context XG*Y, where X and Y are different DNA bases. The G* residues were positioned at or close to the center of 11 base pair (∼1 helical turn) or 16 base pair (∼1.5 turns) duplexes. All bases, except for X and Y and their partners, were identical. These sequences were self-ligated with T4 ligase to form multimers that yield a ladder of bands upon electrophoresis in native polyacrylamide gels. The extent of bending in each oligonucleotide was assessed by monitoring the decrease in gel mobilities of these linear, self-ligated oligomers, relative to unmodified oligonucleotides of the same base sequence. The extent of global bending was then estimated using a sequence-specific three-dimensional model from which the values of the base-pair step parameter roll adjacent to the lesion site could be extracted. We find that (+)-trans-anti-[BP]-N2-dG adducts are considerably more bent than the (−) isomers regardless of sequence and that A-T base pairs flanking the [BP]-N2-dG lesion site allow for local flexibility consistent with adduct conformational heterogeneity. Interestingly, the fit of computed versus observed gel mobilities using classical reptation treatments requires enhancement of unmodified DNA flexibility in gels, compared to aqueous salt solution. The differences in bending between the two stereoisomeric adduct duplexes and the observed base sequence context effects may play a significant role in the differential processing of these lesions by cellular replication, transcription, and repair enzymes.