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Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion

Authors: Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, and Max Wiedenhöft

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract

RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nanoscale RNA structures and has recently been shown to be Turing universal. While post-transcriptional splicing is well studied, co-transcriptional splicing is gaining attention for its efficiency, though its unpredictability still remains a challenge. In this paper, we focus on engineering co-transcriptional splicing, not only as a natural phenomenon but as a programmable mechanism for generating specific RNA target sequences from DNA templates. The problem we address is whether we can encode a set of RNA sequences for a given system onto a DNA template word, ensuring that all the sequences are generated through co-transcriptional splicing. Given that finding the optimal encoding has been shown to be NP-complete under the various energy models considered [Da-Jung Cho et al., 2025], we propose a practical alternative approach under the logarithmic energy model. More specifically, we provide a construction that encodes an arbitrary nondeterministic finite automaton (NFA) into a circular DNA template from which co-transcriptional splicing produces all sequences accepted by the NFA. As all finite languages can be efficiently encoded as NFA, this framework solves the problem of finding small DNA templates for arbitrary target sets of RNA sequences. The quest to obtain the smallest possible such templates naturally leads us to consider the problem of minimizing NFAs and certain practically motivated variants of it, but as we show, those minimization problems are computationally intractable.

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Da-Jung Cho, Szilárd Zsolt Fazekas, Shinnosuke Seki, and Max Wiedenhöft. Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cho_et_al:LIPIcs.DNA.31.5,
  author =	{Cho, Da-Jung and Fazekas, Szil\'{a}rd Zsolt and Seki, Shinnosuke and Wiedenh\"{o}ft, Max},
  title =	{{Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.5},
  URN =		{urn:nbn:de:0030-drops-238548},
  doi =		{10.4230/LIPIcs.DNA.31.5},
  annote =	{Keywords: RNA Transcription, Co-Transcriptional Splicing, Finite Automata Simulation, NFA Minimization}
}

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DOI: 10.4230/LIPIcs.CPM.2025.4

The Equivalence Problem of E-Pattern Languages with Length Constraints Is Undecidable

Authors: Dirk Nowotka and Max Wiedenhöft

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)

Abstract

Patterns are words with terminals and variables. The language of a pattern is the set of words obtained by uniformly substituting all variables with words that contain only terminals. Length constraints restrict valid substitutions of variables by associating the variables of a pattern with a system (or disjunction of systems) of linear diophantine inequalities. Pattern languages with length constraints contain only words in which all variables are substituted to words with lengths that fulfill such a given set of length constraints. We consider membership, inclusion, and equivalence problems for erasing and non-erasing pattern languages with length constraints. Our main result shows that the erasing equivalence problem - one of the most prominent open problems in the realm of patterns - becomes undecidable if length constraints are allowed in addition to variable equality. Additionally, it is shown that the terminal-free inclusion problem, a prominent problem which has been shown to be undecidable in the binary case for patterns without any constraints, is also generally undecidable for all larger alphabets in this setting. Finally, we also show that considering regular constraints, i.e., associating variables also with regular languages as additional restrictions together with length constraints for valid substitutions, results in undecidability of the non-erasing equivalence problem. This sets a first upper bound on constraints to obtain undecidability in this case, as this problem is trivially decidable in the case of no constraints and as it has unknown decidability if only regular or only length constraints are considered.

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Dirk Nowotka and Max Wiedenhöft. The Equivalence Problem of E-Pattern Languages with Length Constraints Is Undecidable. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{nowotka_et_al:LIPIcs.CPM.2025.4,
  author =	{Nowotka, Dirk and Wiedenh\"{o}ft, Max},
  title =	{{The Equivalence Problem of E-Pattern Languages with Length Constraints Is Undecidable}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.4},
  URN =		{urn:nbn:de:0030-drops-230988},
  doi =		{10.4230/LIPIcs.CPM.2025.4},
  annote =	{Keywords: Patterns, Pattern Languages, Length Constraints, Regular Constraints, Decidability, Undecidability, Membership, Inclusion, Equivalence}
}

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Documents authored by Wiedenhöft, Max

Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion

Abstract

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The Equivalence Problem of E-Pattern Languages with Length Constraints Is Undecidable

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