A practical guide to molecular dynamics simulations of DNA origami systems

Jejoong Yoo, Chen Yu Li, Scott Michael Slone, Christopher Maffeo, Aleksei Aksimentiev

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in situ structure and physical properties of DNA origami objects. This chapter provides step-by-step instructions for building atomic-scale models of DNA origami systems, using the MD method to simulate the models, and performing basic analyses of the resulting MD trajectories.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages209-229
Number of pages21
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1811
ISSN (Print)1064-3745

Fingerprint

Molecular Dynamics Simulation
DNA
Nucleic Acids

Keywords

  • Bionanotechnology
  • Computer simulations
  • DNA nanotechnology
  • DNA origami
  • Molecular dynamics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Yoo, J., Li, C. Y., Slone, S. M., Maffeo, C., & Aksimentiev, A. (2018). A practical guide to molecular dynamics simulations of DNA origami systems. In Methods in Molecular Biology (pp. 209-229). (Methods in Molecular Biology; Vol. 1811). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-8582-1_15

A practical guide to molecular dynamics simulations of DNA origami systems. / Yoo, Jejoong; Li, Chen Yu; Slone, Scott Michael; Maffeo, Christopher; Aksimentiev, Aleksei.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 209-229 (Methods in Molecular Biology; Vol. 1811).

Research output: Chapter in Book/Report/Conference proceedingChapter

Yoo, J, Li, CY, Slone, SM, Maffeo, C & Aksimentiev, A 2018, A practical guide to molecular dynamics simulations of DNA origami systems. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1811, Humana Press Inc., pp. 209-229. https://doi.org/10.1007/978-1-4939-8582-1_15
Yoo J, Li CY, Slone SM, Maffeo C, Aksimentiev A. A practical guide to molecular dynamics simulations of DNA origami systems. In Methods in Molecular Biology. Humana Press Inc. 2018. p. 209-229. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-8582-1_15
Yoo, Jejoong ; Li, Chen Yu ; Slone, Scott Michael ; Maffeo, Christopher ; Aksimentiev, Aleksei. / A practical guide to molecular dynamics simulations of DNA origami systems. Methods in Molecular Biology. Humana Press Inc., 2018. pp. 209-229 (Methods in Molecular Biology).
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