Ghetto Sanger Sequencing, Part I

Here are some ruminations about the first steps I'm taking towards a kind of Ghetto Sanger sequencing contraption:
Basically, what I'm trying to build is a setup that will automate some of the steps in Sanger sequencing. One of these steps involves automatically starting a gel electrophoresis, which includes placing the gel into the buffer-filled gel box, firing up the power source, monitoring the gel's progress, shutting down the power source in time and removing the gel from the gel box.
One of the problems here is that gels are somewhat difficult to handle for something like a robotic arm. It's much like trying to transfer a slab of Jell-O into a water bath and then out again.
So my idea was to use plastic slides with gel-filled channels. Let's call them gel slides for short. The material should be non-conductive, transparent, and withstand a certain a mount of heat. Here's a sketch of one, with 8 channels, 6 of them are sketched as being gel-filled:



Initially, I thought I could just cut channels into a piece of acrylic using a laser cutter or CNC mill. Unfortunately, people who know their milling have explained to me that neither is trivial.
So for the first prototype, I used a sandwiched design, with a kind of laser-cut "comb" glued on top of a solid bottom slide. The comb turned out very irregular, which is not good:



It will be a bitch to glue this onto the bottom slide correctly, and since these gel slides will probably be a consumable, this kind of hassle is not really an option. So I'll have to do something differently next time.
I'm thinking about maybe using a design that is closed on both sides rather than just one, but I have no idea whether this would undesirably impact the electric field during electrophoresis.
Also, someone pointed out to me that it might be much better to cast the gel slides rather than cut them. Or, perhaps, there is a much better way to do this altogether. Needs more thinking.

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