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Conjugate word blending: formal model and experimental implementation by XPCR

Abstract

This paper introduces conjugate word blending as a formal model of molecular processes that occur during a DNA experimental protocol called cross-pairing Polymerase Chain Reaction (XPCR). We analyze this formal word and language operation from a computational viewpoint, by investigating closure properties of four Chomsky language families under it. We also report the molecular biology wet lab experiments based on XPCR amplification of gene sequences, which led to the notion of conjugate word blending.

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Notes

  1. 1.

    The length of a DNA double strand is measured in basepairs (bp), whereby 1 bp is a unit consisting of one base on a DNA strand together with its corresponding complementary base on the opposite strand.

  2. 2.

    The opposite process, that of a DNA double strand breaking apart into its constituent single strands, is called melting or denaturation (achieved by increasing the temperature).

  3. 3.

    A chimeric sequence is a sequence formed from the prefix of one sequence and the suffix of another sequence joined together.

  4. 4.

    \(\alpha\) = 5\(^\prime\)-TTCTACAAGGAGGATATTACC-3\(^\prime\), \(\overline{\beta }\) = 5\(^\prime\)-TATGGAGATGTACCTGATATC-3\(^\prime\), \(\gamma\) = 5\(^\prime\)-ATATTGGAGGAGGTATACAAC-3\(^\prime\), \(\overline{\gamma }\) = 5\(^\prime\)-GTTGTATACCTCCTCCAATAT-3\(^\prime\).

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Correspondence to Lila Kari or Silvia Lampis.

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This research was partially supported by NSERC (Natural Sciences and Engineering Research Council of Canada) Discovery Grant R2824A01 and Univ. of Waterloo Transition Grant to L.K., and by FUR (Single Fund for Research), Italian Ministry of Education, Universities, and Research (MIUR) to G.F.

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Cite this article

Bellamoli, F., Franco, G., Kari, L. et al. Conjugate word blending: formal model and experimental implementation by XPCR. Nat Comput 20, 647–658 (2021). https://doi.org/10.1007/s11047-021-09867-x

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Keywords

  • Conjugate word blending
  • Cross-pairing Polymerase Chain Reaction (XPCR)
  • DNA computing
  • Gene assembly
  • Formal language operations
  • Molecular computing
  • Word blending
  • Word operations

Mathematics Subject Classification

  • 68R01
  • 92B99