Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2’-deoxyguanosine (2’dG)-sensing riboswitch from Mesoplasma florum.

核糖开关形成一类丰富的顺式调节RNA元件，通过结合小代谢物来介导基因表达。对于合成生物学应用，它们正在成为廉价且可访问的系统，用于选择性地触发下游基因的转录或翻译。许多核糖开关是受动力学控制的，因此了解其共转录机制至关重要。我们在这里提出了一种有效的实现方式，用于分析共转录RNA-配体的相互作用动力学。这种方法首次允许对浓度依赖性代谢物的结合/解离动力学进行建模。我们通过最近研究的来自中型支原体的IA 2'-脱氧鸟苷（2'dG）-感应核糖开关来举例说明这种新颖的方法。