Chen Jingyang, Dupradeau François-Yves, Case David A, Turner Christopher J, Stubbe JoAnne
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
Biochemistry. 2007 Mar 20;46(11):3096-107. doi: 10.1021/bi6024269. Epub 2007 Feb 27.
A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.
在一个特定的双链DNA序列5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5'（1）中合成了一个4'-氧化脱碱基位点（X）。其结构已通过二维核磁共振方法、分子建模和分子动力学模拟确定。1整体呈B型，与X相对的碱基（A）位于螺旋内且堆积良好。仅观察到X的α异头物，且脱碱基位点的脱氧核糖大部分位于螺旋内。将这些结果与相同序列背景下的正常脱碱基位点（Y）（2）进行了比较。Y由α和β异头物（2α和2β）的60:40混合物组成。在2α和2β中，与Y相对的碱基（A）均位于螺旋内且堆积良好，且脱碱基位点的脱氧核糖主要位于螺旋外，这与在类似序列背景下正常脱碱基位点的报道结构一致[霍恩，S. T.，特纳，C. J.，和斯塔布，J.（2001）核酸研究。29，3413 - 3423]。分子动力学模拟表明，正常脱碱基位点在构象上似乎比4'-氧化脱碱基位点更具灵活性。讨论了脱碱基位点的结构和灵活性在DNA修复酶Ape1识别中的重要性。
