Influence of the single-strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano-cage family

Authors

  • Federico Iacovelli,

    1. Department of Biology, University of Rome “Tor Vergata” and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Rome, Italy
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  • Cassio Alves,

    1. Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo, Brasil
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  • Mattia Falconi,

    1. Department of Biology, University of Rome “Tor Vergata” and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Rome, Italy
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  • Francesco Oteri,

    1. Department of Biology, University of Rome “Tor Vergata” and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Rome, Italy
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  • Cristiano L. P. de Oliveira,

    1. Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo, Brasil
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  • Alessandro Desideri

    Corresponding author
    1. Department of Biology, University of Rome “Tor Vergata” and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Rome, Italy
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

ABSTRACT

The structural/dynamical properties of three truncated octahedral DNA nano-cages composed by identical double helices but single strand linkers with different composition, namely 7 thymidines, 7 adenines, and 7 alternated thymidines and adenines, have been investigated through classical molecular dynamics simulations. Trajectories have been analyzed to investigate the role of the linkers in defining nano-cages stability and flexibility, including possible influence on the internal cages motions. The data indicate that the cages behavior is almost identical and that the structural/dynamical parameters measured along the trajectories are not particularly affected by the presence of different bases. These results demonstrate that the constraints imposed by the nano-structure geometry are the main factor in modulating these properties. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 992–999, 2014.

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