Week of June 7th Summary
Experiments This Week
Monday – 20% SDS-PAGE of both of last week’s rtcB reactions without boiling the samples. Resulted in the appearance of the 20mer. Data still looks peculiar. Two bands in the 10mer lanes, etc.
Tuesday – setup of 3rd o/n rtcB reaction w/ additional controls. P. 62-64, reworked all my calculations. Nanodropped and made stocks of sub 1B – the real 10mer. I had been using sub 2B, a 13mer.
Wednesday – 20% SDS-PAGE of 3rd ligation rxn, with additional controls. Sub 1b runs heavier than the 20mer, with and without protein. Other unusual features continue to persist.
Thursday – designed new RNA substrates, 20mer and DNAzymes to match. Started out using the Raines’s paper’s RNA substrates, but had to change them significantly since the corresponding DNAzymes formed hairpins.
Friday – attempted at 12% SDS-PAGE rtcB gel to confirm that it was not aggregating. Stacking gel failed to polymerize, so I didn’t end up running it.
Purchases for the week = $52.39
Polypropylene does not dissolve in 2-propanol, according to the paper, “Measurement and Correlation of Solubility for Propylene in 2-propanol-water Solutions,” Liu Guo-zhu, et al. (2006).
De-gassing did seem to get rid of the speckles in my gels that I stained with SYBR gold and imaged ~580-630 PMT on the Typhoon.