Fig. 3: Beetroot binding and activation of DFHO and ThT. | Nature Communications

Fig. 3: Beetroot binding and activation of DFHO and ThT.

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

Fig. 3

a DFAME fluorescence in the presence of Beetroot binding site mutants, normalized to wild-type (mean±s.d., n = 5 for A16G, A16U, and U38A; n = 4 for A16C, U38G, U38C, A16G,U38G, and A16U,U38A; n = 3 for A16C,U38G, and A16U,U38G – n denotes independent sample replicate). b Fluorescence activation of four different fluorophores by Beetroot (mean±s.d., n = 3 – n denotes independent sample replicate). c Cartoon representation of the core of the Beetroot–DFHO homodimer complex co-crystal structure. d Cartoon representation of the core of the Beetroot–ThT homodimer complex co-crystal structure. e Detail of the binding site with DFHO. f Orthogonal view of e the binding site of Beetroot–DFHO from the direction of P2. g Detail of the binding site with ThT. h Orthogonal view of g the binding site of Beetroot–ThT from the direction of P2. In e–h gray mesh depicts |Fo | − |Fc| electron density map before building the fluorophores, contoured at 2.0 σ.

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