Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes

Methods Mol Biol. 2021:2167:91-111. doi: 10.1007/978-1-0716-0716-9_7.

Abstract

Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA structure includes taking in account pseudoknots presence in the structure, which is usually a challenge for bioinformatics tools. Our method includes using "Enzymer," a software for designing RNA sequences with desired secondary structures that may include pseudoknots. Enzymer implements an efficient stochastic search and optimization algorithm to sample RNA sequences from low ensemble defect mutational landscape of an initial design template to generate an RNA sequence that is predicted to fold into the desired target structure.

Keywords: GlmS ribozyme; HDV ribozyme; Hammerhead ribozyme; Inverse folding; Pistol ribozyme; Pseudoknot; RNA structure; Synthetic biology; Twister ribozyme; VS ribozyme.

MeSH terms

  • Algorithms
  • Base Sequence
  • Computational Biology / methods*
  • Computer-Aided Design*
  • Electrophoresis, Agar Gel
  • Electrophoresis, Polyacrylamide Gel
  • In Vitro Techniques
  • Kinetics
  • Nucleic Acid Conformation*
  • Nucleotide Motifs / genetics
  • Polymerase Chain Reaction / methods
  • RNA / genetics
  • RNA Folding / genetics
  • RNA, Catalytic / chemistry*
  • RNA, Catalytic / genetics*
  • RNA, Catalytic / metabolism
  • Software
  • Synthetic Biology / methods*
  • Transcription, Genetic

Substances

  • RNA, Catalytic
  • hammerhead ribozyme
  • RNA