This contribution sketches a work flow to design an RNA switch that is able to adapt two structural conformations in a ligand-dependent way. A well characterized RNA aptamer, i.,e., knowing its K_d$K_d$ and adaptive structural features, is an essential ingredient of the described design process. We exemplify the principles using the well-known theophylline aptamer throughout this work. The aptamer in its ligand-binding competent structure represents one structural conformation of the switch while an alternative fold that disrupts the binding-competent structure forms the other conformation. To keep it simple we do not incorporate any regulatory mechanism to control transcription or translation. We elucidate a commonly used design process by explicitly dissecting and explaining the necessary steps in detail. We developed a novel objective function which specifies the mechanistics of this simple, ligand-triggered riboswitch and describe an extensive in silico analysis pipeline to evaluate important kinetic properties of the designed sequences. This protocol and the developed software can be easily extended or adapted to fit novel design scenarios and thus can serve as a template for future needs.

这一贡献勾勒出了设计RNA开关的工作流程，该开关能够以配体依赖性方式适应两个结构构象。表征良好的RNA适体，即知道其K _d${ķ}_d$自适应结构特征是上述设计过程的重要组成部分。在整个工作中，我们使用众所周知的茶碱适体来举例说明原理。适体在其配体结合能力结构中代表开关的一种结构构象，而破坏结合能力结构的替代折叠形成另一种构象。为简单起见，我们没有采用任何调节机制来控制转录或翻译。通过明确地详细解释和解释必要的步骤，我们阐明了一种常用的设计过程。我们开发了一种新颖的目标函数，该函数指定了这种简单的，配体触发的核糖开关的机理，并描述了广泛的计算机模拟分析流水线，以评估设计序列的重要动力学特性。该协议和开发的软件可以轻松扩展或调整以适合新颖的设计方案，因此可以用作将来需求的模板。