Fig. 3: seRNA functional characterization.
From: Selectively expressed RNA molecules as a versatile tool for functionalized cell targeting
a Using two different probes in parallel, qRT-PCR experiments were performed after the transfer of seRNA-eGFP in non-target and target cells for indicated time periods. All values are given with s.d. n = 4 independent experiments. b Cytokine response analysis after transfer of stable double-stranded RNA (dsRNA), full-length (seRNA), and shortened seRNAΔ3-5−eGFP constructs into non-target and target cells. 24 h after transfer, IL-6 expression levels were quantified by qRT-PCR. All values are given with s.d. n = 4 independent experiments. Significance levels of 0.05, 0.01, and 0.001 based on a one-way ANOVA test were displayed with one to three stars. c Based on minimal free energy (MFE) algorithms (RNAfold WebServer), secondary structure predictions were performed for seRNA modules 4 to 6, including a few nucleotides of module 3 (antisense) and 7 (GFP) with three different IRES-blocker sequences (IB1 to IB3). For all constructs, MFE values are indicated. Their eGFP expression levels in non-target cells (neurons) and target cells (U87) are shown (green signal, right). Flow cytometry-based eGFP positive cells (in %) are indicated for IB1-3 in each image. Transfection efficiencies of seRNAΔ3-5−eGFP into non-target and target cells are given as control. Unaffected cell morphology is indicated in phase contrast. All values are given with s.d. Scale bar = 200 µm. n = 4 to 10. d Correlation between DMS reactivities in biological replicates (Pearson-r) and sequencing coverage (lowest number of reads). The orange dot is seRNAΔ3-5−eGFP, and the green dot is seRNA-eGFP. e Arc plot of DMS supported secondary structure predictions for the seRNAΔ3-5−eGFP (selective) and seRNA-eGFP (non-selective) construct with included delta DMS reactivities. Mean, black line; s.d., gray shading. f Heatmap of DMS reactivities at A and C residues for seRNAΔ3-5−eGFP and seRNA-eGFP RNA using a blue-white-red color scheme. Blue, 0; white, 0.5; red, 1.
