Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA.
J Am Chem Soc. 2010 Feb 24;132(7):2120-1. doi: 10.1021/ja909330m.
The base pairs are the contributors to the sequence-dependent recognition of nucleic acids, genetic information storage, and high fidelity of DNA polymerase replication. However, the wobble base pairing, where T pairs with G instead of A, reduces specific base-pairing recognition and compromises the high fidelity of the enzymatic polymerization. Via the selenium atomic probing at the 2-position of thymidine, we have investigated the wobble discrimination by manipulating the steric and electronic effects at the 2-exo position, providing a unique chemical strategy to enhance the base pair specificity. We report here the first synthesis of the novel 2-Se-thymidine ((Se)T) derivative, its phosphoramidite, and the Se-DNAs. Our biophysical and structural studies of the 2-Se-T DNAs reveal that the bulky 2-Se atom with a weak hydrogen-bonding ability can largely increase mismatch discriminations (including T/G wobble and T/C mismatched base pairs) while maintaining the (Se)T/A virtually identical to the native T/A base pair. The 2-Se atom bulkiness and the electronic effect are probably the main factors responsible for the discrimination against the formation of the wobble (Se)T/G base pair. Our investigations provide a potential novel tool to investigate the specific recognition of base pairs, which is the basis of high fidelity during replication, transcription, and translation. Furthermore, this Se-atom-specific substitution and probing are useful for X-ray crystal structure and function studies of nucleic acids.
碱基对是导致核酸序列依赖性识别、遗传信息存储以及 DNA 聚合酶复制高保真度的原因。然而，在摆动碱基配对中，T 与 G 配对而不是 A，这降低了特定碱基对的识别能力，并损害了酶聚合的高保真度。通过在胸腺嘧啶的 2-位进行硒原子探测，我们通过操纵 2-外消旋位置的空间和电子效应来研究摆动配对的差异，为提高碱基对特异性提供了一种独特的化学策略。我们在此报告了新型 2-硒代胸腺嘧啶（(Se)T）衍生物、其亚磷酰胺和 Se-DNA 的首次合成。我们对 2-硒代-T DNA 的生物物理和结构研究表明，具有弱氢键结合能力的庞大 2-硒原子可以大大提高错配识别（包括 T/G 摆动和 T/C 错配碱基对），同时保持 (Se)T/A 与天然 T/A 碱基对几乎相同。2-硒原子的庞大性和电子效应可能是导致对摆动 (Se)T/G 碱基对形成的歧视的主要因素。我们的研究为研究碱基对的特异性提供了一种潜在的新工具，碱基对的特异性是复制、转录和翻译过程中高保真度的基础。此外，这种硒原子特异性取代和探测对于核酸的 X 射线晶体结构和功能研究很有用。
