Transcript design problem of oritatami systems

Yo Sub Han, Hwee Kim, Shinnosuke Seki

Research output: Contribution to journalArticle


RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene. Oritatami model is a computation model of this phenomenon, which lets its sequence (transcript) of beads (abstract molecules) fold cotranscriptionally by the interactions between beads according to its ruleset. We study the problem of designing a transcript that folds into the given conformation using the given ruleset, which is called the transcript design problem. We prove that the problem is computationally difficult to solve (NP-hard). Then we design efficient poly-time algorithms with additional restrictions on the oritatami system.

Original languageEnglish
Pages (from-to)323-335
Number of pages13
JournalNatural Computing
Issue number2
Publication statusPublished - 2020 Jun 1

All Science Journal Classification (ASJC) codes

  • Computer Science Applications

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