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journal article·2022-09-27Open access

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

ACS Nano· Volume 16· Issue 9
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Source abstract

Abstract

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.
Source: openalex_inverted_index · Quality: baseline

Research context

Nanomaterials

OpenAlex topics: Advanced biosensing and bioanalysis techniques · Bacteriophages and microbial interactions · DNA and Nucleic Acid Chemistry

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States

Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States

Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States

Eyring Materials Center, Office of Knowledge Enterprise Development, Arizona State University, Tempe, Arizona 85287, United States

Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States

Funding

Office of Naval Research · U.S. Department of Energy · Division of Advanced Cyberinfrastructure · National Institute of General Medical Sciences · Division of Materials Research

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