Stereochemistry modulates the stability of reduced interstrand cross-links arising from R- and S-α-CH3-γ-OH-1,N2-propano-2′-deoxyguanosine in the 5′-CpG-3′ DNA sequence
Stereochemistry modulates the stability of reduced interstrand cross-links arising from R- and S-α-CH3-γ-OH-1,N2-propano-2′-deoxyguanosine in the 5′-CpG-3′ DNA sequence
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DOI：
10.1021/bi061381h
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发表时间：
2007-03-13
期刊：
影响因子：
2.9
通讯作者：
Stone, Michael P.
中科院分区：
文献类型：
--
作者：
Cho, Young-Jin;Kozekov, Ivan D.;Stone, Michael P.
通过NMR确定5'-CpG-3'序列中5'-Cp-N-2-dG-3'-R-(α)-CH3-丙基-5'-Cp-N-2-dG-3'和5'-Cp-N-2-dG-3'-S-(α)-CH3-丙基-5'-Cp-N-2-dG-3'链间DNA交联的溶液结构光谱学。这些被用作由巴豆醛和乙醛衍生的R-和S-α-CH3-γ-OH-1,N-2-丙脱氧鸟苷加合物产生的相应甲醇胺链间交联的化学稳定替代物。结果解释了 R-和 S-α-CH3-γ-OH-1,N-2-丙脱氧鸟苷加合物在 5'-CpG-3' 序列中链间交联的形成取决于立体化学，有利于 R-α-CH3-γ-OH-1,N-2-丙脱氧鸟苷加合物 [Kozekov, I. D., Nechev, L. V., M. S. 莫斯利、C. M. 哈里斯、C. J. 里佐、M. P. 斯通和 T. M. 哈里斯 (2003) J. Am.化学。苏克。 125、50-61]。受基于 NOE 的距离和经验约束的分子动力学计算表明，5'-Cp-N-2-dG-3'-R-(α)-CH3-丙基-5'-Cp-N-2-dG-3' 和 5'-Cp-N-2-dG-3'-S-(α)-CH3-丙基-5'-Cp-N-2-dG-3' 交联均是位于小沟中，并在串联交联的 C、G 碱基对处保留沃森-克里克氢键。然而，对于5'-Cp-N-2-dG-3'-R-(α)-CH3-丙基-5'-Cp-N-2-dG-3'交联，(α)-CH3基团位于小沟的中心，而对于5'-Cp-N-2-dG-3'-S-(α)-CH3-丙基-5'-Cp-N2-dG-3'交联时，(α)-CH3 基团位于 3' 方向，显示出对 DNA 螺旋的空间干扰。 5'-Cp-N-2-dG-3'-S-(α)-CH3-丙基-5'-Cp-N-2-dG-3'交联表现出较低的热稳定性，如作为温度函数的NMR光谱所证明的。这两个交联在链间三碳交联的构象上也表现出明显的差异，这也可能导致5'-Cp-N-2-dG-3'-S-(α)-CH3-丙基-5'-Cp-N-2-dG-3'交联的表观热力学稳定性较低。
The solution structures of 5'-Cp-N-2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N-2-dG-3' and 5'-Cp-N-2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N-2-dG-3' interstrand DNA cross-links in the 5'-CpG-3' sequence were determined by NMR spectroscopy. These were utilized as chemically stable surrogates for the corresponding carbinolamine interstrand cross-links arising from the crotonaldehyde- and acetaldehyde-derived R- and S-alpha-CH3-gamma-OH-1,N-2-propanodeoxyguanosine adducts. The results provide an explanation for the observation that interstrand cross-link formation in the 5'-CpG-3' sequence by the R- and S-alpha-CH3-gamma-OH-1,N-2-propanodeoxyguanosine adducts is dependent upon stereochemistry, favoring the R-alpha-CH3-gamma-OH-1,N-2-propanodeoxyguanosine adduct [Kozekov, I. D., Nechev, L. V., Moseley, M. S., Harris, C. M., Rizzo, C. J., Stone, M. P., and Harris, T. M. (2003) J. Am. Chem. Soc. 125, 50-61]. Molecular dynamics calculations, restrained by NOE-based distances and empirical restraints, revealed that both the 5'-Cp-N-2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N-2-dG-3' and 5'-Cp-N-2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N-2-dG-3' cross-links were located in the minor groove and retained Watson-Crick hydrogen bonds at the tandem cross-linked C, G base pairs. However, for the 5'-Cp-N-2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N-2-dG-3' cross-link, the (alpha)-CH3 group was positioned in the center of the minor groove, whereas for the 5'-Cp-N-2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link, the (alpha)-CH3 group was positioned in the 3' direction, showing steric interference with the DNA helix. The 5'-Cp-N-2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N-2-dG-3' cross-link exhibited a lower thermal stability as evidenced by NMR spectroscopy as a function of temperature. The two cross-links also exhibited apparent differences in the conformation of the interstrand three-carbon cross-link, which may also contribute to the lower apparent thermodynamic stability of the 5'-Cp-N-2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N-2-dG-3' cross-link.