IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-8-18

Logistics Communications

Streptavidin Magnetic Beads, Take 3-4

 * Trypsinized the beads, in 50uL solution that were retained from yesterday, for four hours @ 37.
 * 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.


 * 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:


 * 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

 * 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 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

(don't have time to complete. will do on sunday).