Computational fluid dynamics of DNA origami folding in microfluidics

Tianyi Hua, Ryan Hartman

Research output: Contribution to journalArticle

Abstract

DNA origami science is a promising field to arrange materials with high precision on a nanometer scale. The field has attracted much attention due to the robust self-assembly, with applications emerging in pharmaceuticals, nano-engineering, and single molecule recognition. In this research, a computational fluid dynamics (CFD) study was performed on various microfluidic reactor designs, including single-phase laminar flow, gas-liquid segmented flow, and single-phase Dean flow reactors. A new DNA origami folding kinetic model was developed, which enables the prediction of the transition of DNA origami crystal structures as well as their distribution throughout each reactor. Folding of the DNA origami is thermodynamically controlled at a higher temperature of 329 K while the kinetics control the folding at a lower temperature of 325 K, with 327 K corresponding to the optimal temperature for rapid constant temperature folding. The influence of the staple strand concentration was also considered for the first time. The liquid slug length (0.5 mm) and the Dean number (De = 100) were optimized to better understand the appropriate microfluidics. Batch PCR vials and microfluidic gas-liquid multiphase flow provide >90% yields of DNA origami faster than other designs and with less polydispersity, which makes the latter attractive for manufacturing scenarios. However, the microfluidic single-phase laminar flow forms DNA origami faster at the cost of polydispersity, which makes it attractive for high-throughput screening of the kinetics and/or in situ characterization studies. Microfluidics has tremendous potential to impact the field of DNA origami science.

Original languageEnglish (US)
Pages (from-to)818-827
Number of pages10
JournalReaction Chemistry and Engineering
Volume4
Issue number5
DOIs
StatePublished - May 1 2019

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Microfluidics
Computational fluid dynamics
DNA
Polydispersity
Laminar flow
Kinetics
Liquids
Gases
Temperature
Multiphase flow
Drug products
Self assembly
Screening
Crystal structure
Throughput
Molecules
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Catalysis
  • Chemistry (miscellaneous)
  • Chemical Engineering (miscellaneous)
  • Process Chemistry and Technology
  • Fluid Flow and Transfer Processes

Cite this

Computational fluid dynamics of DNA origami folding in microfluidics. / Hua, Tianyi; Hartman, Ryan.

In: Reaction Chemistry and Engineering, Vol. 4, No. 5, 01.05.2019, p. 818-827.

Research output: Contribution to journalArticle

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