RNA-As-Graphs Motif Atlas—Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications

Qiyao Zhu, Louis Petingi, Tamar Schlick

Research output: Contribution to journalArticlepeer-review


RNA motif classification is important for understanding structure/function connections and building phylogenetic relationships. Using our coarse-grained RNA-As-Graphs (RAG) representations, we identify recurrent dual graph motifs in experimentally solved RNA structures based on an improved search algorithm that finds and ranks independent RNA substructures. Our expanded list of 183 existing dual graph motifs reveals five common motifs found in transfer RNA, riboswitch, and ribosomal 5S RNA components. Moreover, we identify three motifs for available viral frameshifting RNA elements, suggesting a correlation between viral structural complexity and frameshifting efficiency. We further partition the RNA substructures into 1844 distinct submotifs, with pseudoknots and junctions retained intact. Common modules are internal loops and three-way junctions, and three submotifs are associated with riboswitches that bind nucleotides, ions, and signaling molecules. Together, our library of existing RNA motifs and submotifs adds to the growing universe of RNA modules, and provides a resource of structures and substructures for novel RNA design.

Original languageEnglish (US)
Article number9249
JournalInternational journal of molecular sciences
Issue number16
StatePublished - Aug 2022


  • coarse-grained RNA motifs
  • dual graphs and subgraphs
  • riboswitch structures
  • viral frameshifting elements

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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