8EYV

Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.

(2023) Nat Commun 14: 2969-2969

• PubMed: 37221204 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1038/s41467-023-38683-3
• Primary Citation of Related Structures:  
  8EYU, 8EYV, 8EYW, 8F0N


• PubMed Abstract: 
  

  Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.

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Organizational Affiliation: 

Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.