The thrombin binding aptamer (TBA) is a prototypical platform used to understand the impact of chemically-modified nucleotides on aptamer stability and target affinity. To provide structural insight into the experimentally-observed effects of modification size, location, and number on aptamer performance, long time-scale molecular dynamics (MD) simulations were performed on multiple binding orientations of TBA–thrombin complexes that contain a large, flexible tryptophan thymine derivative (T-W) or a truncated analogue (T-K). Depending on modification position, T-W alters aptamer–target binding orientations, fine-tunes aptamer–target interactions, strengthens networks of nucleic acid–protein contacts, and/or induces target conformational changes to enhance binding. The proximity and 5′-to-3′ directionality of nucleic acid structural motifs also play integral roles in the behavior of the modifications. Modification size can differentially influence target binding by promoting more than one aptamer–target binding pose. Multiple modifications can synergistically strengthen aptamer–target binding by generating novel nucleic acid–protein structural motifs that are unobtainable for single modifications. By studying a diverse set of modified aptamers, our work uncovers design principles that must be considered in the future development of aptamers containing chemically-modified nucleotides for applications in medicine and biotechnology, highlighting the value of computational studies in nucleic acids research.

中文翻译：

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在适配子工程中解锁精度：凝血酶结合适配子的案例研究说明了为什么修饰大小、数量和位置很重要


凝血酶结合适配体 （TBA） 是一个原型平台，用于了解化学修饰的核苷酸对适配体稳定性和靶标亲和力的影响。为了提供关于实验观察到的修饰大小、位置和数量对适配体性能影响的结构见解，对包含大而灵活的色氨酸胸腺嘧啶衍生物 （T-W） 或截短类似物 （T-K） 的 TBA-凝血酶复合物的多个结合方向进行了长时间尺度的分子动力学 （MD） 模拟。根据修饰位置，T-W 会改变适配体-靶标结合方向，微调适配体-靶标相互作用，加强核酸-蛋白质接触网络，和/或诱导靶标构象变化以增强结合。核酸结构基序的接近性和 5' 到 3' 方向性在修饰的行为中也起着不可或缺的作用。修饰大小可以通过促进多个适配体-靶标结合姿势来差异性地影响靶标结合。多重修饰可以通过产生新的核酸-蛋白质结构基序来协同增强适配体-靶标结合，而这些基序是单个修饰无法获得的。通过研究多种修饰的适配子，我们的工作揭示了在未来开发含有化学修饰核苷酸的适配子用于医学和生物技术时必须考虑的设计原则，突出了计算研究在核酸研究中的价值。