Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
Biophys Chem. 2023 Dec;303:107111. doi: 10.1016/j.bpc.2023.107111. Epub 2023 Sep 25.
Understanding the 3-D structure of nucleic acid aptamers is important for the rational design of aptamer-based constructs in various applications, including for developing aptasensors. Herein, a simple approach for 3D modelling of ssDNA aptamers through an ensemble of web applications has been described. The procedure utilized 30 aptamers whose 3D XRD or NMR experimental structures are available for validation. As a first step, the primary sequences of ssDNA aptamers were transformed into 2D structures using six widely used web applications: RNA fold, Vector builder, RNA Structure, UNA fold, Centroid fold, and IP Knot. The generated 2D structures were then passed through the RNA composer web application to generate 3D RNA structure, which in turn was converted to 3D DNA structures using various Visual Molecular Dynamics web applications that also include conversion of ribose sugar into deoxyribose sugar backbone and uracil to thiamine. The energy-minimized generated 3D structures were matched well with high accuracy to their experimental counterparts. This study identified that the Guanine residues are crucial in the aptamer 3D structure prediction and in algorithms that generate secondary structures. Further, the GC content (<50%), GC bond percentage (<60%), and G:C ratio (<1.12) act as limiting factors in predicting the 2D structures of aptamers. There were variations in the 2D structure predictions by the web applications, even though all these applications were a combination of the MFE, MEA, and McCaskill functions. Processing these structures through the web applications described above produced best-fit 3D structures with the experimental one, thus offering the present ensemble approach to reliably predict the 3D structure of aptamers for various applications.
理解核酸适体的 3-D 结构对于基于适体的构建体在各种应用中的合理设计很重要，包括开发适体传感器。在此，描述了一种通过一组网络应用程序对 ssDNA 适体进行 3D 建模的简单方法。该程序利用了 30 个适体的序列，这些适体的 3D XRD 或 NMR 实验结构可用于验证。作为第一步，使用六种广泛使用的网络应用程序将 ssDNA 适体的原始序列转换为 2D 结构：RNA fold、Vector builder、RNA Structure、UNA fold、Centroid fold 和 IP Knot。生成的 2D 结构然后通过 RNA composer 网络应用程序生成 3D RNA 结构，然后使用各种 Visual Molecular Dynamics 网络应用程序将其转换为 3D DNA 结构，其中还包括将核糖糖转换为脱氧核糖糖骨架和尿嘧啶转换为硫胺素。生成的能量最小化的 3D 结构与实验结果高度吻合。该研究确定鸟嘌呤残基在适体 3D 结构预测和生成二级结构的算法中至关重要。此外，GC 含量(<50%)、GC 键百分比(<60%)和 G:C 比(<1.12)是预测适体 2D 结构的限制因素。即使所有这些应用程序都是 MFE、MEA 和 McCaskill 功能的组合，网络应用程序的 2D 结构预测也存在差异。通过上述网络应用程序处理这些结构可以产生与实验结构最匹配的 3D 结构，从而为各种应用提供了可靠预测适体 3D 结构的当前集合方法。
