IGEM:Harvard/2006/DNA nanostructures

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(Notes)
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====Notes====
====Notes====
-
Questions
+
Questions / procedures
* what percent gel? 10% to 20% polyacrylamide gels, no SDS (but would make for a good control)
* what percent gel? 10% to 20% polyacrylamide gels, no SDS (but would make for a good control)
* what incubation conditions?
* what incubation conditions?
* how much protein and DNA? protein at 1 {{um}}, DNA at 2 {{um}}
* how much protein and DNA? protein at 1 {{um}}, DNA at 2 {{um}}
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* DNA in excess
+
* Coomassie stain
* experiments
* experiments
** all combinations protein, aptamer, nanotube
** all combinations protein, aptamer, nanotube

Revision as of 11:34, 10 July 2006

Contents

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

Image:iGEM_harv06_mattspecs.gif

Container Designs

Latch Designs

Coding

Existing code

Thrombin-aptamer experiments

Notes

Questions / procedures

  • what percent gel? 10% to 20% polyacrylamide gels, no SDS (but would make for a good control)
  • what incubation conditions?
  • how much protein and DNA? protein at 1 μM, DNA at 2 μM
  • Coomassie stain
  • experiments
    • all combinations protein, aptamer, nanotube

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]
All Medline abstracts: PubMed HubMed

Presentations

Most recent (Week 3)

Week 2: Original proposal

Working Team Members

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