期刊
NUCLEIC ACIDS RESEARCH
卷 44, 期 7, 页码 3013-3019出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw155
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资金
- National Science Foundation [DMR-1507985, PHY-1430124]
- Direct For Mathematical & Physical Scien
- Division Of Physics [1430124] Funding Source: National Science Foundation
- Division Of Materials Research
- Direct For Mathematical & Physical Scien [1507985] Funding Source: National Science Foundation
The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures.
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