IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-8-18: Difference between revisions
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** A lidless | ** A lidless | ||
=== | ===12 Hours Later=== | ||
* | * Ran gel of proteinase-K-ed final supernatant | ||
* | |||
** | **'''Gel:''' | ||
* | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Lane''' | |||
| align="center" style="background:#f0f0f0;"|'''Component''' | |||
| align="center" style="background:#f0f0f0;"|'''Amount''' | |||
|- | |||
| 1||1kb ladder||1uL (from stock of 1ug/uL) | |||
|- | |||
| 2||p7308||9uL | |||
|- | |||
| 3||6hb wash-supernatant||38uL | |||
|- | |||
| 4||c5.0.8b wash-supernatant||38uL | |||
|- | |||
| 5||c5.0.Eb wash-supernatant||38uL | |||
|- | |||
| 6||c5.0.Fb wash-supernatant||38uL | |||
|- | |||
| 7||6hb final-supernatant||38uL | |||
|- | |||
| 8||c5.0.8b final-supernatant||38uL | |||
|- | |||
| 9||c5.0.Eb final-supernatant||38uL | |||
|- | |||
| 10||c5.0.Fb final-supernatant||38uL | |||
|} | |||
<gallery> | |||
Image:TC-060818-bds-proteinasek.jpg|2% agarose, 10mM MgCl2, 3uL EtBr, 1:10hr @ 80V | |||
</gallery> | |||
**'''Results:''' | |||
***NOTHING in final-supernatant lanes again, indicating either: | |||
****(A) Second trypsinization (not able to be visualized because ran the gel without enough buffer) worked, leaving nothing on the streptavidin for the proteinase K to have digested. | |||
****(B) Proteinase K did not digest the streptavidin to elute. | |||
*** Wash lanes were also dim - did not Speedvac for long enough. | |||
**** Also, gel was older and had been left out of fridge overnight. | |||
*****'''Plan:''' Try again with proteinase K as eluent, as there were so many problems with this trial (ie. "Eb" and "Fb", trypsinization first two times around) | |||
== Folding design 6 == | == Folding design 6 == |
Revision as of 16:31, 19 August 2006
Streptavidin Magnetic Beads, Take 3-4
- Trypsinized the beads, in 50uL solution that were retained from yesterday, for four hours @ 37[[:Category:{{{1}}}|{{{1}}}]].
- Ran gel of them, ladder, and p7308
- Noticed when took the gel out for imaging that the buffer was below the gel slightly - didn't cover top
- Imaging: NO BANDS AT ALL, not for the ladder or even p7308.
- Suspect that the gel didn't run due to too-low-buffer.
- On the off-chance that the trypsin digest didn't work, used 2uL (of unknown activity concentration, see above) of proteinase K to try again to digest the streptavidin.
- Incubated overnight at 37[[:Category:{{{1}}}|{{{1}}}]].
- Mixed c5.0.1 and other pre-working stocks and working stocks listed above.
- Folded 4 rxns each, at intermediate {Mgcl2}} of 20mM final concentration, of:
- E(b)
- F(b)
- A lidless
12 Hours Later
- Ran gel of proteinase-K-ed final supernatant
- Gel:
Lane | Component | Amount |
1 | 1kb ladder | 1uL (from stock of 1ug/uL) |
2 | p7308 | 9uL |
3 | 6hb wash-supernatant | 38uL |
4 | c5.0.8b wash-supernatant | 38uL |
5 | c5.0.Eb wash-supernatant | 38uL |
6 | c5.0.Fb wash-supernatant | 38uL |
7 | 6hb final-supernatant | 38uL |
8 | c5.0.8b final-supernatant | 38uL |
9 | c5.0.Eb final-supernatant | 38uL |
10 | c5.0.Fb final-supernatant | 38uL |
-
2% agarose, 10mM MgCl2, 3uL EtBr, 1:10hr @ 80V
- Results:
- NOTHING in final-supernatant lanes again, indicating either:
- (A) Second trypsinization (not able to be visualized because ran the gel without enough buffer) worked, leaving nothing on the streptavidin for the proteinase K to have digested.
- (B) Proteinase K did not digest the streptavidin to elute.
- Wash lanes were also dim - did not Speedvac for long enough.
- Also, gel was older and had been left out of fridge overnight.
- Plan: Try again with proteinase K as eluent, as there were so many problems with this trial (ie. "Eb" and "Fb", trypsinization first two times around)
- Also, gel was older and had been left out of fridge overnight.
- NOTHING in final-supernatant lanes again, indicating either:
- Results:
Folding design 6
- Mixing pre-working stocks (c6.0.1, c6.0.2, c6.0.3, c6.0.4, c6.0.5)
- To mix pre-working stocks from plates, pipet 10 μL of each of the appropriate oligos into 1.5 mL tubes.
- List of pre-working and working stock oligos: Table_of_c6.0_Working_Stocks