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


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.
Number of pages21
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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