8F0N

Wobble Beetroot (A16U-U38G) dimer bound to DFHO

Summary for 8F0N

• Entry DOI: 10.2210/pdb8f0n/pdb
• Descriptor: RNA (49-MER), POTASSIUM ION, (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one, ... (4 entities in total)
• Functional Keywords: rna, aptamer, fluorescence, turn-on, fluorogenic, fluorophore, g-quartet, g-quadruplex
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 32836.94

Authors

Passalacqua, L.F.M.,Ferre-D'Amare, A.R. (deposition date: 2022-11-03, release date: 2023-05-31, Last modification date: 2023-10-25)

Primary citation

Passalacqua, L.F.M.,Starich, M.R.,Link, K.A.,Wu, J.,Knutson, J.R.,Tjandra, N.,Jaffrey, S.R.,Ferre-D'Amare, A.R.
Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.
Nat Commun, 14:2969-2969, 2023

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.

PubMed: 37221204
DOI: 10.1038/s41467-023-38683-3

Experimental method

X-RAY DIFFRACTION (2.85 Å)