Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein-DNA Nanostructures

Raghu Pradeep Narayanan, Jonah Procyk, Purbasha Nandi, Abhay Prasad, Yang Xu, Erik Poppleton, Dewight Williams, Fei Zhang, Hao Yan, Po Lin Chiu, Nicholas Stephanopoulos, Petr Šulc

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


We present here the combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein-DNA linker identity and length; (2) optimizing the design of protein-DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein-DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable in-silico validation of nanostructured systems before their experimental realization. These tools will facilitate the design of complex hybrid protein-DNA nanostructures that seamlessly integrate the two different biomolecules.

Original languageEnglish (US)
Pages (from-to)14086-14096
Number of pages11
JournalACS nano
Issue number9
StatePublished - Sep 27 2022


  • DNA nanotechnology
  • coarse-grained models
  • cryo-EM fitting
  • molecular dynamics
  • protein-DNA

ASJC Scopus subject areas

  • Materials Science(all)
  • Engineering(all)
  • Physics and Astronomy(all)


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