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Transcript Design Problem of Oritatami Systems

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DNA Computing and Molecular Programming (DNA 2018)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11145))

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Abstract

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.

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Notes

  1. 1.

    For the hardness proof, we use the decision variant of TDP, which determines whether or not such a transcript exists.

  2. 2.

    This definition does not consider any pair both of whose beads are included in \(C_\sigma \) because such a pair is already inert at the beginning of folding.

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Acknowledgements

Han was supported by NRF 2017K2A9A2A08000270 and NRF 2015R1D1A1A01060097, Kim was supported in part by the NIH grant R01 GM109459, and S. S. 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 JSPS Bilateral Program No. YB29004.

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Authors and Affiliations

  1. Department of Computer Science, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea

    Yo-Sub Han

  2. Department of Mathematics and Statistics, University of South Florida, 12010 USF Cherry Drive, Tampa, FL, 33620, USA

    Hwee Kim

  3. Department of Computer and Network Engineering, University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo, 1828585, Japan

    Shinnosuke Seki

Authors
  1. Yo-Sub Han
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  2. Hwee Kim
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  3. Shinnosuke Seki
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Correspondence to Hwee Kim .

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Editors and Affiliations

  1. University of California, Davis, CA, USA

    David Doty

  2. Technical University Munich, Garching, Germany

    Hendrik Dietz

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Han, YS., Kim, H., Seki, S. (2018). Transcript Design Problem of Oritatami Systems. In: Doty, D., Dietz, H. (eds) DNA Computing and Molecular Programming. DNA 2018. Lecture Notes in Computer Science(), vol 11145. Springer, Cham. https://doi.org/10.1007/978-3-030-00030-1_9

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  • DOI: https://doi.org/10.1007/978-3-030-00030-1_9

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-00029-5

  • Online ISBN: 978-3-030-00030-1

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