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Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures

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Part of the Lecture Notes in Computer Science book series (LNTCS,volume 5347)

Abstract

We present the development of a new graphical user interface driven molecular modeling, editing and visualization tool called Tiamat. Tiamat addresses the challenge of how to efficiently model large and complex DNA nanostructures. We describe the three major components of our system. First, we discuss design guidelines and data structures that form the basis of flexible and large-scale editing. Second, we explain a semi-automatic sequence generator that combines user input with random sequence generation to efficiently label the molecules in the DNA structure. Third, we outline the visualization techniques including a simplification algorithm that are used to render large designs. The results demonstrate how Tiamat was used to generate large and complex designs.

Keywords

  • Structural DNA nanotechnology
  • DNA tile
  • 3D DNA structure display
  • DNA sequence design

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Williams, S., Lund, K., Lin, C., Wonka, P., Lindsay, S., Yan, H. (2009). Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures. In: Goel, A., Simmel, F.C., Sosík, P. (eds) DNA Computing. DNA 2008. Lecture Notes in Computer Science, vol 5347. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03076-5_8

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  • DOI: https://doi.org/10.1007/978-3-642-03076-5_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-03075-8

  • Online ISBN: 978-3-642-03076-5

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