Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers

Abstract

Fluorescence turn-on aptamers,in vitroevolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA–fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.

Rapid deployment of smartphone‐based augmented reality tools for field and online education in structural biology

“…[6][7][8][9] Students compare the structures of the fluorophores present in each structure and the suppression of twisted intramolecular charge transfer (TICT) by which the protein and aptamer activate the fluorescence of their respective fluorophores. 10 In the 2016 and 2017 iterations of the module, we used PyMol exclusively for this purpose. In the 2018 and 2019 iterations of the module, we added the AR portion described here.…”

Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?

“…However, since a minimal portion of the human genome is translated into proteins while most of it is transcribed into RNA, being able to investigate the dynamic and spatial properties of the human transcriptome has become essential. As there are no known naturally fluorescent RNAs, a series of in vitro engineered ribonucleic tags able to fold into peculiar three-dimensional structures were selected (Trachman and Ferré-D'Amaré, 2019). These RNAs, through an aptameric domain, can bind fluorophore molecules, increasing their spectroscopic signal and hence allowing for the dynamic monitoring of nucleic acid expression and localization in cells.…”

Repurposing Antiviral Drugs for Orthogonal RNA‐Catalyzed Labeling of RNA

“…Site‐specific labeling of RNA by covalent attachment of a bioorthogonal functional group or fluorescent reporter is of fundamental importance for biochemical and biophysical studies and in the areas of cellular and synthetic biology . Non‐covalent labeling of RNA has been pursued by fluorogen‐activating aptamers that are inserted into the RNA of interest as large fluorescent tags . Covalent labeling with small organic fluorophores through bioorthogonal linkages has several advantages.…”