Fig. 3: RNA structure library for ligand interactions and DNA barcode microarray for quantification.
From: RNA structure-wide discovery of functional interactions with multiplexed RNA motif library
a In silico molecular design for the RNA structure library. Extracted RNA structures are conjugated to the stabilizing stem structure and RNA barcodes for massively parallel quantification of each RNA in the library. After the addition of the T7 promoter sequence, reverse complementary DNA sequences are synthesized as an oligo pool. See also Supplementary Fig. 1 and Methods. b Schematic of the barcode-based hybridization on a custom DNA microarray. Each spot on the microarray contains DNA sequences complementary to one barcode region of the RNA probe in the library. c In vitro preparation of the RNA structure library. The single-stranded DNA (ssDNA) templates in the pool have anti-T7 promoter sequences that can hybridize to the T7 promoter ssDNA. In turn, the T7 polymerase produces the RNA structures in a single tube. In vitro transcription generates the library in a single tube from the oligo DNA pool. The subsequent RNA ligation attaches a fluorescent dye to the 3′ end of the RNA probes for detection and quantification.
