Journal
ACS NANO
Volume -, Issue -, Pages -Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acsnano.2c04013
Keywords
DNA nanotechnology; protein-DNA; cryo-EM fitting; coarse-grained models; molecular dynamics
Categories
Funding
- NSF [1931487]
- ONR [N000142012094]
- National Science Foundation [1753387]
- National Institute of General Medical Sciences of the National Institutes of Health [DP2GM132931]
- US Department of Energy [DE-SC0002423]
- Division Of Materials Research
- Direct For Mathematical & Physical Scien [1753387] Funding Source: National Science Foundation
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [1931487] Funding Source: National Science Foundation
- U.S. Department of Defense (DOD) [N000142012094] Funding Source: U.S. Department of Defense (DOD)
- U.S. Department of Energy (DOE) [DE-SC0002423] Funding Source: U.S. Department of Energy (DOE)
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This study presents a combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. The tools can optimize the design and validate experimental results, facilitating the design of complex nanostructures.
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 insilico 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.
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