DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

Carsten Svaneborg, Harold Fellermann, Steen Rasmussen

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Abstract

We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can hybridize reversibly. Along with the dynamic hybridization bonds, angular and dihedral bonds are dynamically introduced and removed to model the collective properties of double helix structure on the DNA zippering dynamics. We use this DNA model to simulate the temperature dependent self-assembly of DNA tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation.
Original languageEnglish
Title of host publicationDNA Computing and Molecular Programming
PublisherSpringer
Publication date2012
Pages123-134
ISBN (Print)978-3-642-32207-5
ISBN (Electronic)978-3-642-32208-2
DOIs
Publication statusPublished - 2012
EventInternational Conference on DNA Computing and Molecular Programming - Århus, Denmark
Duration: 14. Aug 201217. Aug 2012

Conference

ConferenceInternational Conference on DNA Computing and Molecular Programming
Country/TerritoryDenmark
CityÅrhus
Period14/08/201217/08/2012
SeriesLecture Notes in Computer Science
Volume7433
ISSN0302-9743

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