Suresh Gorle, Padhi Siladitya, Patil Indrajit, Priyakumar U Deva
Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032, India.
Biochemistry. 2016 Oct 11;55(40):5653-5664. doi: 10.1021/acs.biochem.6b00309. Epub 2016 Sep 29.
Urea lesions are formed in DNA because of free radical damage of the thymine base, and their occurrence in DNA blocks DNA polymerases, which has deleterious consequences. Recently, it has been shown that urea is capable of forming hydrogen bonding and stacking interactions with nucleobases, which are responsible for the unfolding of RNA in aqueous urea. Base pairing and stacking are inherent properties of nucleobases; because urea is able to form both, this study attempts to investigate if urea can mimic nucleobases in the context of nucleic acid structures by examining the effect of introducing urea lesions complementary to the four different nucleobases on the overall helical integrity of B-DNA duplexes and their thermodynamic stabilities using molecular dynamics (MD) simulations. The MD simulations resulted in stable duplexes without significant changes in the global B-DNA conformation. The urea lesions occupy intrahelical positions by forming hydrogen bonds with nitrogenous nucleobases, in agreement with experimental results. Furthermore, these urea lesions form hydrogen bonding and stacking interactions with other nucleobases of the same and partner strands, analogous to nucleobases in typical B-DNA duplexes. Direct hydrogen bond interactions are observed for the urea-purine pairs within DNA duplexes, whereas two different modes of pairing, namely, direct hydrogen bonds and water-mediated hydrogen bonds, are observed for the urea-pyrimidine pairs. The latter explains the complexities involved in interpreting the experimental nuclear magnetic resonance data reported previously. Binding free energy calculations were further performed to confirm the thermodynamic stability of the urea-incorporated DNA duplexes with respect to pure duplexes. This study suggests that urea mimics nucleobases by pairing opposite all four nucleobases and maintains the overall structure of the B-DNA duplexes.
由于胸腺嘧啶碱基的自由基损伤，DNA中会形成尿素损伤，而其在DNA中的出现会阻碍DNA聚合酶，从而产生有害后果。最近的研究表明，尿素能够与核碱基形成氢键和堆积相互作用，这是尿素水溶液中RNA解折叠的原因。碱基配对和堆积是核碱基的固有特性；由于尿素能够形成这两种相互作用，本研究试图通过分子动力学（MD）模拟，研究引入与四种不同核碱基互补的尿素损伤对B-DNA双链体整体螺旋完整性及其热力学稳定性的影响，以探讨尿素在核酸结构背景下是否能模拟核碱基。MD模拟结果显示双链体稳定，整体B-DNA构象无显著变化。尿素损伤通过与含氮核碱基形成氢键占据螺旋内位置，这与实验结果一致。此外，这些尿素损伤与同一条链和互补链的其他核碱基形成氢键和堆积相互作用，类似于典型B-DNA双链体中的核碱基。在DNA双链体中，尿素-嘌呤对存在直接氢键相互作用，而尿素-嘧啶对则观察到两种不同的配对模式，即直接氢键和水介导的氢键。后者解释了先前报道的实验核磁共振数据解释中的复杂性。进一步进行结合自由能计算，以确认含尿素的DNA双链体相对于纯双链体的热力学稳定性。本研究表明，尿素通过与所有四种核碱基配对来模拟核碱基，并维持B-DNA双链体的整体结构。
