Rational design of oligonucleotides for enhanced in vitro transcription of small RNA

Overview of the ROCKET software. (A) Cloverleaf structures of Thermoplasma acidophilum tRNA^Leu, Thermus thermophilus tRNA^Pro, and T. kodakarensis tRNA^His. (B) Workflow for computational design of DNA oligonucleotides for in vitro transcription. (C) Oligonucleotide selection for T. acidophilum tRNA^Lue. The number of usable oligonucleotides is narrowed down in ROCKET in subsequent steps. (D) The ΔG_total (ΔG_{forward oligo} + ΔG_{forward oligo}) was calculated for each set of forward/reverse oligonucleotides. The suboptimal oligonucleotide set with the lowest (dark-gray) and the optimal set with the highest ΔG_total value (orange) are highlighted.