IGEM:Harvard/2006/DNA nanostructures

From OpenWetWare

Project Overview

• Our goal is to to design and implement molecular containers, which can be dynamically opened and closed by an external stimulus.
• The containers will be implemented as DNA nanostructures, which afford a significant degree of positional control and chemical versatility.
• As an initial proof-of-concept, we plan to use our DNA containers to demonstrate controllable activation ("delivery") of anti-thrombin aptamers.
• We expect that molecular containers could have several interesting scientific and clinical applications, such as
  • Drug and gene delivery
  • Bio-marker scavenging (early detection of biomarkers)
  • Directed evolution (compartmentalized selections)
  • Using multiplexing for combinatorial chemical synthesis
  • Capture and stabilization of multiprotein complexes
  • Protein folding (chaperones)
  • Cell sorting

Container Specs

Container Designs

Design 1 hexagonal core, separate 1-ply lids

Design 2 hexagonal core, separate 2-ply lids

Design 3 rectangular core, continuous 1-ply lids

Design 4 hexagonal core, separate 1-ply lids

Latch Designs

latch1 (ai file)

latch2 (ai file)

Coding

Existing code

• William's code (Python)

Thrombin-aptamer experiments

Notes

Buffers

• Macaya's and Bock's selection buffer: 20 mM Tris-acetate, pH 7.4, 140 mM NaCl / 5 mM KCl / 1 mM CaCl₂ / 1 mM MgCl₂

Bibliography

1. Schultze P, Macaya RF, and Feigon J. . pmid:8107090. PubMed HubMed [tha1]
2. Liu Y, Lin C, Li H, and Yan H. . pmid:15945116. PubMed HubMed [tha2]
3. Li WX, Kaplan AV, Grant GW, Toole JJ, and Leung LL. . pmid:8298130. PubMed HubMed [tha3]
4. Bock LC, Griffin LC, Latham JA, Vermaas EH, and Toole JJ. . pmid:1741036. PubMed HubMed [tha4]
5. Macaya RF, Schultze P, Smith FW, Roe JA, and Feigon J. . pmid:8475124. PubMed HubMed [tha5]

Presentations

Most recent (Week 3)

• Week 3 Presentation: Design Progress

Week 2: Original proposal

• Presentation Proposal

Working Team Members

• Tiffany Chan (talk)
• Katherine Fifer (talk)
• Valerie Lau (talk)
• Matthew Meisel (talk)
• ...and others are welcome!