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DNA Rearrangements through Spatial Graphs

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Book cover Programs, Proofs, Processes (CiE 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6158))

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Abstract

The paper is a short overview of a recent model of homologous DNA recombination events guided by RNA templates that have been observed in certain species of ciliates. This model uses spatial graphs to describe DNA rearrangements and show how gene recombination can be modeled as topological braiding of the DNA. We show that a graph structure, which we refer to as an assembly graph, containing only 1- and 4-valent rigid vertices can provide a physical representation of the DNA at the time of recombination. With this representation, 4-valent vertices correspond to the alignment of the recombination sites, and we model the actual recombination event as smoothing of these vertices.

Research supported in part by the NSF grants CCF-0726396 and DMS-0900671.

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Author information

Authors and Affiliations

  1. Department of Mathematics and Stataistics, University of South Florida, USA

    Nataša Jonoska & Masahico Saito

Authors
  1. Nataša Jonoska
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  2. Masahico Saito
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Editor information

Editors and Affiliations

  1. Departamento de Matemática, Universidade de Lisboa, Campo Grande, Edifício C6, 1749-016, Lisboa, Portugal

    Fernando Ferreira

  2. Institute for Logic, Language and Computation (ILLC), Universiteit van Amsterdam, P.O. Box 94242, 1090, Amsterdam, GE, The Netherlands

    Benedikt Löwe

  3. Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, María de Luna 1, 50018, Zaragoza, Spain

    Elvira Mayordomo

  4. Universidade dos Açores, Campus de Ponta Delgada, Apartado 1422, 9501-801, Ponta Delgada, Açores, Portugal

    Luís Mendes Gomes

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© 2010 Springer-Verlag Berlin Heidelberg

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Jonoska, N., Saito, M. (2010). DNA Rearrangements through Spatial Graphs. In: Ferreira, F., Löwe, B., Mayordomo, E., Mendes Gomes, L. (eds) Programs, Proofs, Processes. CiE 2010. Lecture Notes in Computer Science, vol 6158. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13962-8_24

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  • DOI: https://doi.org/10.1007/978-3-642-13962-8_24

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13961-1

  • Online ISBN: 978-3-642-13962-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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