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DNA Nanostructures

Nicholas Gangi, Maya Modi, and Stephanya Moran

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Introduction

Pray, L. (2008) Discovery of DNA structure and function: Watson and Crick. Nature Education 1(1):100

DNA Double Helix

DNA Cube

DOI: 10.1016/S1369-7021(03)00129-9

DNA Nanotechnology

  • Drug Delivery
  • Nanotechnology
  • Analysis of Molecular Compounds

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5 Steps to Make 2D Shapes

Long strands of DNA self-assemble into a complex shape, which is held in place by smaller stabilizing strands called “staples”

  1. Build geometric model made of double-stranded DNA
  2. Fold single-stranded DNA into model
  3. Design set of “staples” with computer program
  4. Alter “staple” locations to minimize strain
  5. Merge adjacent or nearby “staples” and finalize locations

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DOI: 10.1038/nature04586

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5.

2.

4.

3.

1.

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Branched Points

DOI:10.1016/S1369-7021(03)00129-9

  • Form intersections between DNA strands
  • Important part of more complicated structures
  • Example: the 2D array being formed on the right
  • Holliday Junction

DOI: 10.1016/B978-0-12-262430- 8.50006-1

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Scaling Up the Process - DNA Algorithms

  • Algorithms are used to generate 2D and 3D shapes
  • caDNAno (Figures E and F)
  • DAEDALUS (Figure J)
  • vHelix (Figure K)

DOI: 10.1016/j.chempr.2017.02.009

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DNA Nanostructures

Triple Crossover

Octahedron

DOI: 10.1016/j.apmt.2015.11.004

DOI: 10.1038/nature02307

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Need for DNA Nanotechnology

DOI: 10.3390/chemosensors6020016

Top Down Fabrication:

  • Start with large structure and reshape it through tools to achieve desired structure
  • Difficult to achieve on a nanoscale

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Bottom Up Fabrication:

  • Use natural intermolecular forces to induce self assembly of molecules into desired structure
  • Good for nanoscale

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Nanoelectronics - Nanowires

Single Wall Carbon Nanotube oriented by DNA

DOI: 10.1038/420761a

DOI: 10.1073/pnas.0305860101

DNA Nanotubes can be metalized to form wires

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Biosensors

DOI: doi.org/10.1021/acsnano.8b01510

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Imaging Using Nanostructures

DNA Cages being used for the imaging of molecules

DNA Cages being used for the imaging of molecules

DOI: 10.1016/S1369-7021(03)00129-9

DOI: 10.1016/j.jconrel.2016.08.013

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Drug Delivery

  • Nanosized DNA structures are used to deliver bioactive compounds
    • Include: cage-like structures, particle structures, polypods, hydrogels
  • Advantages
    • Good structural programmability
    • Excellent permeability
    • Great biocompatibility

DOI: 10.3389/fphar.2019.01585

Cage-like structures

Hydrogels

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Protein Nanotechnology

Benefits:

  • Size precision
  • Use templates from nature to minimize complexity of assembly

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Limitations:

  • Protein-protein interface is a delicate issue
  • Creates typical box and unit-lattice structure

DOI: doi.org/10.1021/acs.biomac.9b00228

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Polysaccharide Nanotechnology

Benefits:

  • Immunogenicity (produces an immune response)
  • High sensitivity to stimuli (pH, ion strength, heat, magnetism, light)

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Limits:

  • Safety hazards due to extra refinement processes
  • Immunogenicity

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DOI: 10.1515/ntrev-2012-0050

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Nanotechnology - Comparisons

  • DNA nanotechnology is more programmable, biocompatible, modifiable (by precise chemical process), and easier/safer to use
  • Biggest limitation: not dynamic (we can make buildings but not robots)

DOI: doi.org/10.1016/j.chempr.2017.02.009

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Current, Evolving Projects

  • Newer method: DNA brick self-assembly
    • Uses short synthetic strands of DNA like Legos to form 2D and 3D structures
  • Dynamic DNA structures
    • DNA robots
  • COVID Testing!!!
    • Biosensors/DNA chips could be used for mass rapid testing