Negi Indu, Kathuria Preetleen, Sharma Purshotam, Wetmore Stacey D
Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.
Phys Chem Chem Phys. 2017 Jun 28;19(25):16365-16374. doi: 10.1039/c7cp02576a.
Computational (DFT and MD simulation) methods are employed to systematically characterize the structural and energetic properties of five hydrophobic nucleobases (FEMO, MMO2, NaM, 5SICS and TPT3) that constitute four unnatural base pairs (FEMO:5SICS, MMO2:5SICS, NaM:5SICS and TPT3:NaM). These hydrophobic bases have been recently shown to be replicated when present between natural bases in DNA duplexes, with the highest replication fidelity and efficiency occuring for the TPT3:NaM pair. Our QM calculations suggest that the preferred (anti) glycosidic orientations of nucleosides containing hydrophobic bases are similar to the natural DNA nucleosides despite differences in their chemical structures. However, due to the inability to form interbase hydrogen bonds, hydrophobic base pairs intrinsically prefer nonplanar, distorted geometries, many of which are stabilized through π-π stacking interactions. Furthermore, the intrinsic stacking potential between a hydrophobic and a natural base is similar to that between two natural bases, indicating that the strength of stacking interactions in DNA duplexes containing hydrophobic bases is likely comparable to natural DNA. However, in contrast to the isolated base-pair geometries, our MD simulations suggest that the hydrophobic base pairs adopt variable geometries within DNA, which range from stacked (5SICS:FEMO) to nearly planar (5SICS:NaM and SICS:MMO2) to planar (TPT3:NaM). As a result, the duplex structural features at the site of modification depend on the identity of the hydrophobic base pair, where the TPT3:NaM pair causes the least structural changes compared to natural DNA. Overall, the structural insight obtained from our calculations on DNA containing hydrophobic base pairs explains the experimentally-observed higher fidelity and efficiency during replication of TPT3:NaM compared to other hydrophobic nucleobase pairs. By providing valuable structural information that explains the intrinsic and duplex properties of this class of unnatural nucleobases, the present work may aid the future design of improved hydrophobic analogues.
采用计算（密度泛函理论和分子动力学模拟）方法系统地表征了构成四个非天然碱基对（FEMO:5SICS、MMO2:5SICS、NaM:5SICS和TPT3:NaM）的五个疏水核碱基（FEMO、MMO2、NaM、5SICS和TPT3）的结构和能量性质。最近研究表明，当这些疏水碱基存在于DNA双链体的天然碱基之间时能够被复制，其中TPT3:NaM碱基对的复制保真度和效率最高。我们的量子力学计算表明，尽管含疏水碱基的核苷化学结构存在差异，但其优选的（反式）糖苷取向与天然DNA核苷相似。然而，由于无法形成碱基间氢键，疏水碱基对本质上更倾向于非平面、扭曲的几何结构，其中许多结构通过π-π堆积相互作用得以稳定。此外，疏水碱基与天然碱基之间的内在堆积势与两个天然碱基之间的相似，这表明含疏水碱基的DNA双链体中堆积相互作用的强度可能与天然DNA相当。然而，与孤立的碱基对几何结构不同，我们的分子动力学模拟表明，疏水碱基对在DNA中采用可变几何结构，范围从堆积结构（5SICS:FEMO）到近平面结构（5SICS:NaM和SICS:MMO2）再到平面结构（TPT3:NaM）。因此，修饰位点处的双链体结构特征取决于疏水碱基对的特性，与天然DNA相比，TPT3:NaM碱基对引起的结构变化最小。总体而言，我们对含疏水碱基对的DNA计算所获得的结构见解解释了实验观察到的TPT3:NaM与其他疏水核碱基对相比在复制过程中具有更高保真度和效率的现象。通过提供有价值的结构信息来解释这类非天然核碱基的内在性质和双链体性质，本研究可能有助于未来设计出改良的疏水类似物。
