IGEM:Harvard/2006/DNA nanostructures/Notebook: Difference between revisions
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<li>[[IGEM:Harvard/2006/ | <li>[[IGEM:Harvard/2006/DNA nanostructures|Project Overview]]</li> | ||
<li>[[IGEM:Harvard/2006/ | <li>[[IGEM:Harvard/2006/DNA_nanostructures/Designs|Designs]]</li> | ||
<li id="current">[[IGEM:Harvard/2006/DNA_nanostructures/Notebook| | <li id="current">[[IGEM:Harvard/2006/DNA_nanostructures/Notebook|Notebook]]</li> | ||
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Protocols| | <li>[[IGEM:Harvard/2006/DNA_nanostructures/Protocols|Protocols]]</li> | ||
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Literature| | <li>[[IGEM:Harvard/2006/DNA_nanostructures/Presentations|Presentations]]</li> | ||
<li>[[IGEM:Harvard/2006/DNA_nanostructures/Literature|Literature]]</li> | |||
</ul> | </ul> | ||
</div> | </div> | ||
<br style="clear:both"> | <br style="clear:both"> | ||
< | |||
==Daily notebook== | |||
<calendar> | |||
name=IGEM:Harvard/2006/DNA_nanostructures/Notebook | |||
date=2006/07/01 | |||
view=threemonths | |||
format=%name/%year-%month-%day | |||
weekstart=7 | |||
</calendar> | |||
<calendar> | |||
name=IGEM:Harvard/2006/DNA_nanostructures/Notebook | |||
date=2006/10/01 | |||
view=threemonths | |||
format=%name/%year-%month-%day | |||
weekstart=7 | |||
</calendar> | |||
==General Notes== | |||
*'''Stock Oligos''': reconstituted (50uM for non-biotinylated oligos, 200uM for biotinylated) oligos in wells or tubes | |||
*'''Pre-working Stocks''': mixtures of 10uM of each oligo needed for a "class" of oligos (ex. core, barrel, lid1, lid2); for non-biot oligos, this requires 10uL of each of the necessary stock oligos, for biot-oligos, this requires 2.5uL of stock oligos + 7.5uL dH2O | |||
*'''Working Stocks''': mixtures of however-many-oligos-are-in-each-class uL (ex. if there are 94 oligos in the core class of 3.2's design, use 94uL of the core pre-working stock), diluted to a total of 200uL of solution (each individual oligo will be at 250nM) | |||
==Brainstorming and future projects== | |||
===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> |
Latest revision as of 17:10, 5 September 2006
Daily notebook
<calendar> name=IGEM:Harvard/2006/DNA_nanostructures/Notebook date=2006/07/01 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar>
<calendar> name=IGEM:Harvard/2006/DNA_nanostructures/Notebook date=2006/10/01 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar>
General Notes
- Stock Oligos: reconstituted (50uM for non-biotinylated oligos, 200uM for biotinylated) oligos in wells or tubes
- Pre-working Stocks: mixtures of 10uM of each oligo needed for a "class" of oligos (ex. core, barrel, lid1, lid2); for non-biot oligos, this requires 10uL of each of the necessary stock oligos, for biot-oligos, this requires 2.5uL of stock oligos + 7.5uL dH2O
- Working Stocks: mixtures of however-many-oligos-are-in-each-class uL (ex. if there are 94 oligos in the core class of 3.2's design, use 94uL of the core pre-working stock), diluted to a total of 200uL of solution (each individual oligo will be at 250nM)
Brainstorming and future projects
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+