The Chili RNA aptamer is a 52 nt long fluorogen-activating RNA aptamer (FLAP) that confers fluorescence to structurally diverse derivatives of fluorescent protein chromophores. A key feature of Chili is the formation of highly stable complexes with different ligands, which exhibit bright, highly Stokes-shifted fluorescence emission. In this work, we have analyzed the interactions between the Chili RNA and a family of conditionally fluorescent ligands using a variety of spectroscopic, calorimetric and biochemical techniques to reveal key structure–fluorescence activation relationships (SFARs). The ligands under investigation form two categories with emission maxima of ∼540 or ∼590 nm, respectively, and bind with affinities in the nanomolar to low-micromolar range. Isothermal titration calorimetry was used to elucidate the enthalpic and entropic contributions to binding affinity for a cationic ligand that is unique to the Chili aptamer. In addition to fluorescence activation, ligand binding was also observed by NMR spectroscopy, revealing characteristic signals for the formation of a G-quadruplex only upon ligand binding. These data shed light on the molecular features required and responsible for the large Stokes shift and the strong fluorescence enhancement of red and green emitting RNA–chromophore complexes.
Chili RNA适配体是一种长达52个核苷酸的荧光激活RNA适配体(FLAP),它可以将荧光蛋白色团的结构多样性衍生物赋予荧光。Chili的一个关键特征是与不同配体形成高度稳定的复合物,这些复合物表现出明亮、高Stokes位移的荧光发射。在这项工作中,我们使用各种光谱、热力学和生化技术分析了Chili RNA与一系列有条件荧光配体之间的相互作用,以揭示关键的结构-荧光激活关系(SFARs)。所研究的配体分为两类,分别具有∼540或∼590 nm的发射极大值,并以纳摩尔至低微摩尔的亲和力结合。等温滴定量热法被用来阐明唯一适用于Chili适配体的阳离子配体的焓和熵对结合亲和力的贡献。除了荧光激活外,还通过NMR光谱观察到配体结合,揭示了仅在配体结合时形成G四链体的特征信号。这些数据揭示了红色和绿色发射RNA-色团复合物的大Stokes位移和强荧光增强所需和负责的分子特征。