IGEM:Harvard/2006/DNA nanostructures

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* Macaya's and Bock's selection buffer: 20 mM Tris-acetate, pH 7.4, 140 mM NaCl / 5 mM KCl / 1 mM CaCl<sub>2</sub> / 1 mM MgCl<sub>2</sub>
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* Macaya's and Bock's selection buffer: 20 mM Tris-acetate, pH 7.4, 140 mM NaCl, 5 mM KCl, 1 mM CaCl<sub>2</sub>, 1 mM MgCl<sub>2</sub>
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* Liu's buffer: 40 mM Tris, 20 mM CH<sub>3</sub>COOH, 2mM EDTA, 12.5 mM (CH<sub>3</sub>COO)<sub>2</sub>Mg, pH 8.0
====Bibliography====
====Bibliography====

Revision as of 12:48, 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
  • Liu's buffer: 40 mM Tris, 20 mM CH3COOH, 2mM EDTA, 12.5 mM (CH3COO)2Mg, pH 8.0

Bibliography

Error fetching PMID 8107090:
Error fetching PMID 15945116:
Error fetching PMID 8298130:
Error fetching PMID 1741036:
Error fetching PMID 8475124:
  1. Error fetching PMID 8107090: [tha1]
  2. Error fetching PMID 15945116: [tha2]
  3. Error fetching PMID 8298130: [tha3]
  4. Error fetching PMID 1741036: [tha4]
  5. Error fetching PMID 8475124: [tha5]
All Medline abstracts: PubMed HubMed

Presentations

Most recent (Week 3)

Week 2: Original proposal

Working Team Members

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