I discovered a flaw in my design!
Resolution: I may have dodged a bullet
THING 1: Integrated DNA Technologies (IDT), from whom I buy my DNA, has a special order one can place for long substrates that I didn't notice before. It's cheaper!
EXPLANATION: Long substrates are expensive to purchase because synthesizing them is hard. And mine is long. The first order I made for the substrate I'm using was over $100, because one can only synthesize about 200 nucleotides before synthesis is prohibitory. If in each addition of a nucleotide one has an 80% reaction yield ... well, reaction yield quickly goes down exponentially the more nucleotides one adds. The yield has to be nearly 99.9% to get anywhere. IDT somehow has another option called "ultra" that lets me buy a tiny amount of substrate for much less - $81! I was overjoyed.
THING 2: Another good thing that fell out was that I decided to order DNAzymes from the literature and build my new substrate AROUND them, instead of designing new ones myself.
EXPLANATION: This was for the reason that, though one might use the same DNAzyme reactive core, different binding arms can affect the reactivity. I didn't know that two weeks ago. Researchers have done some kinetics studies on some DNAzymes already and I can know these will be more reliable. I picked some of the fastest ones I could find that would also cleave the most RNA. It wasn't easy to pick, but I did my best.
The course now - onward charge!
What I was up to this past week
M-Tu: Literature searching for new working DNAzymes and designing the new substrate around them. Ordered the new DNAzymes, substrate and splint on Tu.
W: Ordered DNAzymes with eight nucleotide arms. Literature searched and planned for future experiments. Helped Weiwei run a gel. Started on completing Quartzy inventory.
Th: Ran an rtcB protein gel with the cell pellet and lysates. The protein had precipitated though. My substrates came in. Worked on the inventory.
F: Nanodropped all my stocks. Built my DNA ladder. Made fresh stocks for use and Nanodropped those. Imaged my protein gel and dried it on a frame over the weekend.