IGEM:Harvard/2006/DNA nanostructures/Notebook

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==Daily notebook==
<calendar>
<calendar>
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weekstart=14
weekstart=14
</calendar>
</calendar>
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==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?
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* how much protein and DNA? protein at 1 {{um}}, DNA at 2 {{um}}
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* Coomassie stain
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 +
====Experiments====
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{| {{table}}
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| align="center" style="background:#f0f0f0;"|number
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| align="center" style="background:#f0f0f0;"|thrombin
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| align="center" style="background:#f0f0f0;"|aptamer
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| align="center" style="background:#f0f0f0;"|nanotube
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| align="center" style="background:#f0f0f0;"|DNA-stained prediction
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| align="center" style="background:#f0f0f0;"|protein-stained prediction
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|-
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|0||-||-||-||no bands||no bands
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|-
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|1||-||-||+||slow band (nanotube)||no bands
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|-
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|2||-||+||-||fast band (aptamer)||no bands
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|-
 +
|3||-||+||+||slow band (aptamer-nanotube), traces of fast band (aptamer)||no bands
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|-
 +
|4||+||-||-||no bands||fast band (thrombin)
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|-
 +
|5||+||-||+||slow band (nanotube)||fast band (thrombin)
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|-
 +
|6||+||+||-||medium band (aptamer-thrombin), fast band (aptamer)||medium band (aptamer-thrombin), traces of fast band (thrombin)
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|-
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|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)
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|-
 +
|}
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====Buffers====
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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 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 16:48, 11 July 2006


Contents

Daily notebook

June
SMTWTFS
45678910
11121314151617
18192021222324
252627282930
July
SMTWTFS
2345678
9101112131415
16171819202122
23242526272829
3031
August
SMTWTFS
6789101112
13141516171819
20212223242526
2728293031


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 bandsno 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 bandsfast 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+
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