Transcript design problem of oritatami systems
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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.
KeywordsOritatami system Self-assembly RNA cotranscriptional folding Optimization
Han is supported by the Basic Science Research Program through NRF (2018R1D1A1A09084107) and the International Cooperation Program managed by NRF of Korea (2017K2A9A2A08000270). Kim is partially supported by NIH R01GM109459, and by NSF’s CCF-1526485 and DMS-1800443. Kim is also partially supported by the Southeast Center for Mathematics and Biology, an NSF-Simons Research Center for Mathematics of Complex Biological Systems, under National Science Foundation Grant No. DMS-1764406 and Simons Foundation Grant No. 594594. Seki is supported in part by JST Program to Disseminate Tenure Tracking System, MEXT, Japan, No. 6F36, JSPS Grant-in-Aid for Young Scientists (A) No. 16H05854 and for Challenging Research (Exploratory) No. 18K19779, and JSPS-NRF Bilateral Program No. YB29004.
- Bonnet É, Rzażewski P, Sikora F (2018) Designing RNA secondary structures is hard. In: Proceedings of the 22nd annual international conference on research in computational molecular (RECOMB), pp 248–250Google Scholar
- Churkin A, Retwitzer MD, Reinharz V, Ponty Y, Waldispühl J, Barash D (2017) Design of RNAs: comparing programs for inverse RNA folding. Brief Bioinform 19(2):350–358Google Scholar
- Demaine ED, Hendricks J, Olsen M, Patitz MJ, Rogers TA, Schabanel N, Seki S, Thomas H (2018) Know when to fold ’em: self-assembly of shapes by folding in oritatami. In: Proceedings of the 24th international conference on dna computing and molecular programming (DNA), pp 19–36Google Scholar
- Geary CW, Meunier P, Schabanel N, Seki S (2016) Programming biomolecules that fold greedily during transcription. In: Proceedings of the 41st international symposium on mathematical foundations of computer science (MFCS), pp 43:1–43:14Google Scholar
- Geary CW, Meunier P, Schabanel N, Seki S (2018) Proving the turing universality of oritatami co-transcriptional folding. In: Proceedings of the 29th international symposium on algorithms and computation (ISAAC), pp 23:1–23:13Google Scholar
- Han Y, Kim H (2017) Ruleset optimization on isomorphic oritatami systems. In: Proceedings of the 23rd international conference on DNA computing and molecular programming (DNA), pp 33–45Google Scholar
- Han Y, Kim H (2018) Construction of geometric structure by oritatami system. In: Proceedings of the 24th international conference on DNA computing and molecular programming (DNA), pp 173–188Google Scholar