A ribose modification of Spinach aptamer accelerates lead(ii) cation association in vitro

Recent Development of Fluorescent Light-Up RNA Aptamers

Technologies for RNA imaging in live cells play an important role in understanding the function and regulatory process of RNAs. One approach for genetically encoded fluorescent RNA imaging involves fluorescent light-up aptamers (FLAPs), which are short RNA sequences that can bind cognate fluorogens and activate their fluorescence greatly. Over the past few years, FLAPs have emerged as genetically encoded RNA-based fluorescent biosensors for the cellular imaging and detection of various targets of interest. In this review, we first give a brief overview of the development of the current FLAPs based on various fluorogens. Then we further discuss on the photocycles of the reversibly photoswitching properties in FLAPs and their photostability. Finally, we focus on the applications of FLAPs as genetically encoded RNA-based fluorescent biosensors in biosensing and bioimaging, including RNA, non-nucleic acid molecules, metal ions imaging and quantitative imaging. Their design strategies and recent cellular applications are emphasized and summarized in detail.

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More

The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.

A Broccoli aptamer chimera yields a fluorescent K+ sensor spanning physiological concentrations

The RNA aptamer Broccoli accepts 2'fluorinated (2'F) pyrimidine nucleotide incorporation without perturbation of structure or fluorescence in the presence of potassium and DFHBI. However, the modification decreases Broccoli's apparent affinity for K⁺ >30-fold. A chimera of Broccoli RNAs with mixed chemistries displays linear fluorescent gain spanning physiological K⁺ concentrations, yielding an effective RNA-based fluorescent K⁺ sensor.

Subtle sequence variations alter tripartite complex kinetics and G-quadruplex dynamics in RNA aptamer Broccoli

Though extensively utilized, the fluorescent RNA aptamer Broccoli is poorly characterized with an unknown structure. Spectroscopic and kinetic investigations of tripartite complex formation reveal surprising differences between Broccoli and Spinach aptamers despite extreme sequence conservation. Our studies highlight how subtle sequence variations impart functional consequences of G-quadruplex-cation interactions in RNA.