Oligonucleotides selected by ROCKET enhance transcription yields. (A) Secondary structures of T. kodakarensis tRNAHis with nucleotides highlighted in blue that form the annealing region for published forward/reverse oligonucleotides (left) or for oligonucleotide pairs selected by ROCKET as optimal (right) or suboptimal (center). (B) Transcription yields from the one-pot reaction of DNA extension and RNA transcription were monitored by staining of RNA with Toluidine blue after 10% denaturing PAGE (7 M urea) (left) and quantified (right), as described in the Materials and Methods. Errors (x), SD, and P-values are shown. (C) In vitro transcription yields with comparable amounts of template DNA. Errors, SD (n = 3), and P-values are shown.
