IGEM:Harvard/2006/DNA nanostructures: Difference between revisions

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==Thrombin-aptamer experiments==
==Thrombin-aptamer experiments==


====Notes====
====Questions / procedures====
 
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?
Line 43: Line 41:
* Coomassie stain
* Coomassie stain


Experiments
====Experiments====
{| {{table}}
{| {{table}}
| align="center" style="background:#f0f0f0;"|number
| align="center" style="background:#f0f0f0;"|number
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|}
|}


Buffers
====Buffers====
* 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>
* 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>
* Liu's incubation 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
* Liu's incubation 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
* Liu's PAGE buffer: 1x TAE/Mg<sup>2+</sup>
* Liu's PAGE buffer: 1x TAE/Mg<sup>2+</sup>


Potential procedure for 10 {{ul}} incubation reaction
====Protocols====
* In 1 0.2 mL PCR tube, mix:
 
Potential protocol for 10 {{ul}} incubation reaction
* In a 0.2 mL PCR tube, mix:
** 2 {{ul}} of 5x Bock's selection buffer
** 2 {{ul}} of 5x Bock's selection buffer
** 2 {{ul}} of 10 {{um}} scaffold DNA (final concentration: 2 {{um}} = 20 pmol)
** 2 {{ul}} of 10 {{um}} scaffold DNA (final concentration: 2 {{um}} = 20 pmol)
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* Load onto a non-denaturing polyacrylamide gel (10% to 20% gradient)
* Load onto a non-denaturing polyacrylamide gel (10% to 20% gradient)
** Liu runs at 25 mA for 48 h.
** Liu runs at 25 mA for 48 h.
[[User:Matthewmeisel|Matthewmeisel]] 17:13, 10 July 2006 (EDT)


====Bibliography====
====Bibliography====

Revision as of 14:13, 10 July 2006

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 1
    hexagonal core, separate 1-ply lids

  • Design 2 hexagonal core, separate 2-ply lids

    Design 2
    hexagonal core, separate 2-ply lids

  • Design 3 rectangular core, continuous 1-ply lids

    Design 3
    rectangular core, continuous 1-ply lids

  • Design 4 hexagonal core, separate 1-ply lids

    Design 4
    hexagonal core, separate 1-ply lids

Latch Designs

Coding

Existing code

Thrombin-aptamer experiments

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

number thrombin aptamer nanotube DNA-stained prediction protein-stained prediction
0 - - - no bands no bands
1 - - + slow band (nanotube) no bands
2 - + - fast band (aptamer) no bands
3 - + + slow band (aptamer-nanotube), traces of fast band (aptamer) no bands
4 + - - no bands fast band (thrombin)
5 + - + slow band (nanotube) fast band (thrombin)
6 + + - medium band (aptamer-thrombin), fast band (aptamer) medium band (aptamer-thrombin), traces of fast band (thrombin)
7 + + + very slow band (thrombin-aptamer-nanotube), slow band (aptamer-nantotube), traces of fast band (aptamer) very slow band (thrombin-aptamer-nanotube), medium band (aptamer-thrombin), traces of fast band (thrombin)

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 incubation buffer: 40 mM Tris, 20 mM CH3COOH, 2mM EDTA, 12.5 mM (CH3COO)2Mg, pH 8.0
  • Liu's PAGE buffer: 1x TAE/Mg2+

Protocols

Potential protocol for 10 μL incubation reaction

  • In a 0.2 mL PCR tube, mix:
    • 2 μL of 5x Bock's selection buffer
    • 2 μL of 10 μM scaffold DNA (final concentration: 2 μM = 20 pmol)
    • 2 μL of 10 μM oligos (final concentration: 2 μM = 20 pmol)
    • 2 μL of 10 μM aptamers (final concentration: 2 μM = 20 pmol)
    • 2 μL of 5 μM thrombin (final concentration: 1 μM = 10 pmol)
  • Alternative mix: Liu uses 10 pmol (1 μL of 10 μM) and varies thrombin from 2 pmol (1 μL of
  • Incubate at room temperature for 30 min.
  • Load onto a non-denaturing polyacrylamide gel (10% to 20% gradient)
    • Liu runs at 25 mA for 48 h.

Matthewmeisel 17:13, 10 July 2006 (EDT)

Bibliography

  1. Schultze P, Macaya RF, and Feigon J. Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). J Mol Biol. 1994 Feb 4;235(5):1532-47. DOI:10.1006/jmbi.1994.1105 | PubMed ID:8107090 | HubMed [tha1]
  2. Liu Y, Lin C, Li H, and Yan H. Aptamer-directed self-assembly of protein arrays on a DNA nanostructure. Angew Chem Int Ed Engl. 2005 Jul 11;44(28):4333-8. DOI:10.1002/anie.200501089 | PubMed ID:15945116 | HubMed [tha2]
  3. Li WX, Kaplan AV, Grant GW, Toole JJ, and Leung LL. A novel nucleotide-based thrombin inhibitor inhibits clot-bound thrombin and reduces arterial platelet thrombus formation. Blood. 1994 Feb 1;83(3):677-82. PubMed ID:8298130 | HubMed [tha3]
  4. Bock LC, Griffin LC, Latham JA, Vermaas EH, and Toole JJ. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature. 1992 Feb 6;355(6360):564-6. DOI:10.1038/355564a0 | PubMed ID:1741036 | HubMed [tha4]
  5. Macaya RF, Schultze P, Smith FW, Roe JA, and Feigon J. Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3745-9. DOI:10.1073/pnas.90.8.3745 | PubMed ID:8475124 | HubMed [tha5]

All Medline abstracts: PubMed | HubMed

Presentations

Most recent (Week 3)

Week 2: Original proposal

Working Team Members

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