Determining the origin of the stabilization of DNA by 5-aminopropynylation of pyrimidines
Determining the origin of the stabilization of DNA by 5-aminopropynylation of pyrimidines
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DOI：
10.1021/bi047561d
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发表时间：
2005-03-29
期刊：
影响因子：
2.9
通讯作者：
Lane, AN
中科院分区：
文献类型：
--
作者：
Booth, J;Brown, T;Lane, AN
DNA双链体通过嘧啶在5位的氨基丙炔基修饰来稳定。作为离子强度，NMR和分子建模的函数的热力学分析的组合已被应用于确定稳定的起源。对带有一个、两个或三个不相邻的修饰dU和dC的十二聚体以及Dickerson-Drew十二聚体中的单个dU（8）的UV熔融研究表明，修饰在T-m、Δ G和Δ H方面基本上是加和的，并且dU和dC之间几乎没有差异。自由能的变化被解析成静电和非静电组件，这表明在生理离子强度的电荷相互作用的显着贡献，但也是一个非静电的贡献，部分来自水合作用。经修饰的Dickerson-Drew十二聚体的NMR光谱显示，双链体的构象没有被修饰显著改变，尽管P-31 NMR显示正电荷可能影响与相邻磷酸盐的氧原子的离子相互作用。改性的双链体在大沟和小沟中都显示出显著的水合作用。还通过NMR分析了单链，其显示了修饰的寡核苷酸中显著的堆积相互作用的证据。解析能量贡献表明，静电和水合可以产生热力学稳定性的实质性增加，而不会显着改变双链体状态的构象。这些考虑对于用于杂交的寡核苷酸的设计具有重要意义。
DNA duplexes are stabilized by aminopropynyl modification of pyrimidines at the 5 position. A combination of thermodynamic analyses as a function of ionic strength, NMR, and molecular modeling has been applied to determine the origin of the stabilization. UV melting studies of a dodecamer bearing one, two, or three nonadjacent modified dU and dC and of a single dU(8) in the Dickerson-Drew dodecamer revealed that the modifications are essentially additive in terms of T-m, Delta G, and Delta H, and there is little difference between dU and dC. The free energy change was parsed into electrostatic and nonelectrostatic components, which showed a significant contribution from charge interactions at physiological ionic strength but also a nonelectrostatic contribution that arises in part from hydration. NMR spectroscopy of the modified Dickerson-Drew dodecamer revealed that the conformation of the duplexes is not significantly altered by the modifications, though P-31 NMR shows that the positive charge may affect ionic interactions with the oxygen atoms of the neighboring phosphates. The modified duplex showed significant hydration in both major and minor grooves. The single strands were also analyzed by NMR, which showed evidence of significant stacking interactions in the modified oliconucteotide. Parsing the energy contribution has shown that electrostatics and hydration can produce Substantial increases in thermodynamic stability without significant changes in the conformation of the duplex state. These considerations have significance for the design of oligonucleotides used for hybridization.