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

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<div class="tabs-blue">
<ul>
<li id="current">[[IGEM:Harvard/2006/DNA nanostructures|Project Overview]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Designs|Designs]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Notebook|Notebook]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Protocols|Protocols]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Presentations|Presentations]]</li>
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Literature|Literature]]</li>
</ul>
</div>
<br style="clear:both">
==Project Overview==
==Project Overview==
*Our goal is to to design and implement molecular containers, which can be dynamically opened and closed by an external stimulus.
*Our goal is 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.
*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.
*As an initial proof-of-concept, we plan to use our DNA containers to demonstrate controllable activation ("delivery") of anti-thrombin aptamers.
Line 12: Line 25:
**Cell sorting
**Cell sorting


==Container Specs==
==Working Team Members==
[[Image:iGEM_harv06_mattspecs.gif]]
*[[User:TChan|Tiffany Chan]] ([[User_talk:TChan|talk]], [[Special:Contributions/TChan|edits]])
*[[User:Kfifer|Katherine Fifer]] ([[User_talk:Kfifer|talk]], [[Special:Contributions/Kfifer|edits]])
*[[User:Vlau|Valerie Lau]] ([[User_talk:Vlau|talk]], [[Special:Contributions/Vlau|edits]])
*[[User:Matthewmeisel|Matthew Meisel]] ([[User_talk:Matthewmeisel|talk]], [[Special:Contributions/Matthewmeisel|edits]])
*[[User:Lhahn|Lewis Hahn]] ([[User_talk:Lhahn|talk]], [[Special:Contributions/Lhahn|edits]])
*TA: [[User:ShawnDouglas|Shawn Douglas]] ([[User_talk:ShawnDouglas|talk]], [[Special:Contributions/ShawnDouglas|edits]])


==Container Designs==
==Recent Changes==
<gallery>
{{Special:Recentchanges/b=IGEM:Harvard/2006/DNA_nanostructures/&limit=20}}
Image:Igemharv06_Katie_Val_cylinderI.gif|[[IGEM:Harvard/2006/Container Design 1|Design 1]]<br>hexagonal core, separate 1-ply lids
Image:Smallcontainerdesign2.jpg|[[IGEM:Harvard/2006/Container Design 2|Design 2]]<br>hexagonal core, separate 2-ply lids
Image:Igemharv06_msmrect.png|[[IGEM:Harvard/2006/Container Design 3|Design 3]]<br>rectangular core, continuous 1-ply lids
Image:Websmallbarrsingleply.jpg|[[IGEM:Harvard/2006/Container Design 4|Design 4]]<br>hexagonal core, separate 1-ply lids
</gallery>
 
==Latch Designs==
<gallery>
Image:iGEM_harv06_mattlatch1.jpg |latch1 <br>[[:Media:iGEM_harv06_mattlatch1.jpg|jpg]] | [[:Media:IGEM_harv06_mattlatch1.ai|ai]]
Image:iGEM_harv06_mattlatch2.jpg |latch2 <br>[[:Media:iGEM_harv06_mattlatch2.jpg|jpg]] | [[:Media:IGEM_harv06_mattlatch2.ai|ai]]
</gallery>
 
==Coding==
===Existing code===
*[[IGEM:Harvard/2006/DNA_nanostructures/Designing_DNA_nanostructures|William's code (Python)]]
 
==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 {{um}}, DNA at 2 {{um}}
* Coomassie stain
 
====Experiments====
{| {{table}}
| align="center" style="background:#f0f0f0;"|number
| align="center" style="background:#f0f0f0;"|thrombin
| align="center" style="background:#f0f0f0;"|aptamer
| align="center" style="background:#f0f0f0;"|nanotube
| align="center" style="background:#f0f0f0;"|DNA-stained prediction
| align="center" style="background:#f0f0f0;"|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 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 PAGE buffer: 1x TAE/Mg<sup>2+</sup>
 
====Protocols====
 
Potential protocol for 10 {{ul}} incubation reaction
* Reconsitute lyophilized [http://www.sigmaaldrich.com/catalog/search/ProductDetail/SIAL/T6634 bovine thrombin]
** biuret is 745 NIH units = 637 {{ug}} (1170 NIH units = 1 mg)
** "A suggested concentration for preparation of a stock solution is 100 units/ml. The solution should contain approximately 0.1% BSA for stability and is stable for about one week at 0-5 °C. Since thrombin solutions adsorb to glass, it is recommended to aliquot the solution in plastic tubes and store at -20 °C or below." [http://www.sigmaaldrich.com/sigma-aldrich/product_information_sheet/t6634pis.pdf]
** Reconstitute 745 NIH units in 98 {{ul}} 1% BSA and 882 {{ul}} water (0.98 mL total) to give a working stock of 760 units / mL = 650 {{ug}} / mL = 10 nmol / mL = 10 {{um}} (formula weight is approximately 65 kDa) [http://www.sigmaaldrich.com/sigma-aldrich/product_information_sheet/t6634pis.pdf]
* In a 0.2 mL PCR tube, mix:
** 2 {{ul}} of 5x [[IGEM:Harvard/2006/Stock_solutions#Bock.27s_selection_buffer|Bock's selection buffer]]
** 2 {{ul}} of 10 {{um}} scaffold DNA (final concentration: 2 {{um}} = 20 pmol)
** 2 {{ul}} of 10 {{um}} oligos (final concentration: 2 {{um}} = 20 pmol)
** 2 {{ul}} of 10 {{um}} aptamers (final concentration: 2 {{um}} = 20 pmol)
** 1 {{ul}} of 10 {{um}} thrombin (final concentration: 1 {{um}} = 10 pmol)
** 1 {{ul}} of dH<sub>2</sub>O
* Alternative mix: Liu uses 10 pmol of DNA (1 {{ul}} of 10 {{um}}) and varies thrombin amount from 2 pmol (1 {{ul}} of 0.2x thrombin working stock) to 100 pmol (1 {{ul}} of 10x thrombin working stock)
* 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.
[[User:Matthewmeisel|Matthewmeisel]] 17:52, 10 July 2006 (EDT)
 
====Bibliography====
<biblio>
# tha1 pmid=8107090
# tha2 pmid=15945116
# tha3 pmid=8298130
# tha4 pmid=1741036
# tha5 pmid=8475124
</biblio>
 
==Presentations==
 
===Most recent (Week 3)===
* [[Media:IGEMHarv06 Week3 presentation VKTM2.ppt|Week 3 Presentation: Design Progress]]
 
===Week 2: Original proposal===
* [[IGEM:Harvard/2006/DNA_nanostructures/Presentation_proposal|Presentation Proposal]]
 
==Working Team Members==
*[[User:TChan|Tiffany Chan]] ([[User_talk:TChan|talk]])
*[[User:Kfifer|Katherine Fifer]] ([[User_talk:Kfifer|talk]])
*[[User:Vlau|Valerie Lau]] ([[User_talk:Vlau|talk]])
*[[User:Matthewmeisel|Matthew Meisel]] ([[User_talk:Matthewmeisel|talk]])
*...and others are welcome!

Latest revision as of 18:15, 28 October 2006



Project Overview

  • Our goal is 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

Working Team Members

Recent Changes

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