Designing, Building, and Using DNA Nanoboxes: InsideOutside Specific Protection of Sites

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Designing, Building, and Using DNA Nanoboxes
-Inside-Outside Specific Protection of Sites-

• Tiffany Chan
• -
• Harvard International Genetically Engineered
  Machines (iGEM) Team

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1. Intro to DNA Nanoboxes

• WHAT Building DNA nanostructures that act as
  boxes
• -
• WHY Boxes as drug-delivery vehicles
• -
• HOW
• Staple-oligonucleotides single-stranded
  scaffold DNA DNA origami!
• -
• Honeycomb lattice system

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HOW DNA Nanostructures
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2. The Process Designing and Building a DNA
Nanobox

• Coming up with ideas
• lllustrator diagrams
• ASCII diagrams for program inputs
• Schematics of the oligo-scaffold hybridizations
• Running the program to get a list of oligos
• Organizing oligos
• Ordering oligos (with any necessary
  modifications)
• Making up oligo solutions
• Folding the oligos and scaffold to make the
  structure
• Imaging through gel shifts and electron
  micrography

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A C Ideas and Pictures

• A. Coming up with ideas B. lllustrator
  diagrams C. ASCII diagrams for program
  inputs

Double-ply hexagonal barrel, smaller so no lids
necessary?
Single-ply rectangular barrel, lids extending
from barrel?
Single-ply hexagonal barrel, two lids on the
same scaffold?
Double-ply hexagonal barrel, two lids on a
separate scaffold?
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3. Using DNA Nanoboxes

• GOAL Make sure theyre actually boxes!
• A box defines a separate inside and outside
• -
• SOLUTION Protection assays
• Protect what on the inside?
• Thrombin (stuck to thrombin DNA-aptamers built
  into the oligos
• Streptavidin (stuck to the biotin molecules on
  the oligos ordered that way)
• Oligo-ligand (a double-stranded DNA segment made
  from a ssDNA staple-end and a ssDNA added to the
  box mixture after folding)
• From what on the outside?
• Proteases (trypsin and proteinase K)
• Restriction enzyme (AscIII)

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4. Future Plans

• More designs
• More protection assays
• More electron microscopy

snakes on a grid
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THE END!