Difference between revisions of "IGEM:Harvard/2006/DNA nanostructures/Notebook"

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==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>
 

Revision as of 12:47, 11 July 2006


<calendar> name=IGEM:Harvard/2006/DNA_nanostructures/Notebook date=2006/07/01 view=threemonths format=%name/%year-%month-%day weekstart=14 </calendar>