Fig. 3: Circularization efficiency for challenging RNA sequences can be augmented using DNA splints and optimized by applying FRET probes and molecular modeling.
From: Chemical circularization of in vitro transcribed RNA for exploring circular mRNA design
A The predicted MFE secondary structure of RNA11 aligned with the tested DNA splints (ON1–4) and tertiary structure model of a selected fragment (predicted with RNAfold web server). Numbers 1–4 mark the regions of hypothetical interactions between RNA and the splints (Supplementary Table 2). B Fluorescence emission spectra (ex. 500 nm) of a FRET probe (Cy5-RNA11-Cy3) after hybridization with oligonucleotide splints (ON1–4, Supplementary Table 2) or without splint (w/o), recorded at 4 °C or 20 °C. C PAGE analysis of the chemical products of RNA11 circularization, preformed after annealing the precursor with (ON1–4, Supplementary Table 2) or without (w/o) an oligonucleotide splint. S refers to the untreated precursor. Content of mRNA species was quantified densitometrically using CLIQS (Core Laboratory Image Quantification Software). Data presented is representative of one independent experiment.
