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The fidelity of annealing-ligation: A theoretical analysis

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DNA Computing (DNA 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2054))

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Abstract

Understanding the nature of the error propagation through successive biosteps is critical to modeling the overall fidelity of computational DNA architectures. In this work, the fidelity of the compound biostep annealing-ligation is discussed in the limit of zero dissociation, within the framework of a simple statistical thermodynamic model. For simplicity, a DNA ligase of ideal infidelity is assumed, with its error behavior taken as bounding that of real DNA ligases. The derived expression for the fidelity of annealing-ligation indicates that the error coupling is both strong and dependent on sequence. Estimates of the fidelities of annealing and annealing-ligation have also been calculated for various encodings of Adleman’s graph, assuming a staggered zipper model of duplex formation. Results indicate the necessity of including information regarding the specific free energies and/or occupancies of accessible duplex states, in addition to information based purely on sequence comparison.

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Author information

Authors and Affiliations

  1. Institute of Physics, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo, 153, Japan

    John A. Rose

  2. Department of Computer Science and Computer Engineering, The University of Arkansas, Fayetteville, Ark, 72701, USA

    Russell J. Deaton

Authors
  1. John A. Rose
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  2. Russell J. Deaton
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., Canada, V6T 1Z4

    Anne Condon

  2. Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands

    Grzegorz Rozenberg

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© 2001 Springer-Verlag Berlin Heidelberg

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Rose, J.A., Deaton, R.J. (2001). The fidelity of annealing-ligation: A theoretical analysis. In: Condon, A., Rozenberg, G. (eds) DNA Computing. DNA 2000. Lecture Notes in Computer Science, vol 2054. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44992-2_16

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  • DOI: https://doi.org/10.1007/3-540-44992-2_16

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42076-7

  • Online ISBN: 978-3-540-44992-8

  • eBook Packages: Springer Book Archive

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