A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data

  • Damien LarivièreEmail author
  • Rodrigo Galindo-Murillo
  • Eric Fourmentin
  • Samuel Hornus
  • Bruno Lévy
  • Julie Papillon
  • Jean-François Ménétret
  • Valérie LamourEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1624)


The structural modeling of a macromolecular machine is like a “Lego” approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data.

Key words

DNA modeling software Cryo-electron microscopy Molecular dynamics Protein Data Bank Macromolecular complex 

Supplementary material

Video 1

(MP4 28,413 kb)


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Damien Larivière
    • 1
    Email author
  • Rodrigo Galindo-Murillo
    • 2
  • Eric Fourmentin
    • 1
  • Samuel Hornus
    • 3
  • Bruno Lévy
    • 3
  • Julie Papillon
    • 4
  • Jean-François Ménétret
    • 4
  • Valérie Lamour
    • 4
    • 5
    Email author
  1. 1.Fourmentin-Guilbert Scientific FoundationNoisy-le-GrandFrance
  2. 2.Department of Medicinal Chemistry, College of PharmacyUniversity of UtahSalt Lake CityUSA
  3. 3.Equipe Alice, Inria Nancy – Grand EstVillers-lès-NancyFrance
  4. 4.IGBMC, Integrated Structural Biology DepartmentUMR7104 CNRS, U964 Inserm, Université de StrasbourgIllkirchFrance
  5. 5.Hôpitaux Universitaires de StrasbourgStrasbourgFrance

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