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. 2021 Jul 31;13(8):1517. doi: 10.3390/v13081517

Figure 3.

Figure 3

SFV Cp specifically binds a stem loop found within site #1 RNA. (a) Sequence alignment of site #1, StmLp, and StmLpMutant RNAs. Red nucleotides indicate mutated residues. Blue nucleotides indicate residues that make up the predicted stem loop in the WT* structure. (b) mFold secondary structure predictions of site #1 (WT, WT*), StmLp, and StmLpMutant RNAs. The predicted stem loop structures in WT* and StmLp are the same, and are disrupted in the StmLpMutant. WT, WT*, StmLp, and StmLpMutant ∆G = −0.70, −0.70, −0.80, and −3.50 kcal/mol, respectively. (c) 50 ng of site #1, StmLp, and StmLpMutant RNAs analyzed by Urea-PAGE and SYBR Gold. (d) SFV Cp binding to Alexa488-labeled site #1, StmLp, and StmLpMutant RNAs, −/+ poly(I:C). Data points represent the average from n = 3 independent experiments. Error bars represent the standard deviation. Data points are fit with nonlinear regression specific binding with Hill slope in Prism.