Structural Principles of Fluorescent RNA Aptamers

  • Trends Pharmacol Sci. 2017 Oct;38(10):928-939. doi: 10.1016/j.tips.2017.06.007.
Robert J Trachman 3rd  1 ,  Lynda Truong  1 ,  Adrian R Ferré-D'Amaré  2
Affiliations
  • 1. Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
  • 2. Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA. Electronic address: [email protected].
PMID: 28728963 DOI: 10.1016/j.tips.2017.06.007
Abstract

Several aptamer RNAs have been selected in vitro that bind to otherwise weakly fluorescent small molecules and enhance their fluorescence several thousand-fold. By genetically tagging cellular RNAs of interest with these Aptamers and soaking cells in their cell-permeable cognate small-molecule fluorophores, it is possible to use them to study RNA localization and trafficking. These Aptamers have also been fused to metabolite-binding RNAs to generate fluorescent biosensors. The 3D structures of three unrelated fluorogenic RNAs have been determined, and reveal a shared reliance on base quadruples (tetrads) to constrain the photo-excited chromophore. The structural diversity of fluorogenic RNAs and the chemical diversity of potential fluorophores to be activated are likely to yield a variety of future fluorogenic RNA tags that are optimized for different applications in RNA imaging and in the design of fluorescent RNA biosensors.

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