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Murphy joined me for lunch today

A project log for DIY Space Grade DNA Analyzer

Detect DNA non optically by measuring the electrical properties of analytes as they pass by a detector

chuck-glasserChuck Glasser 07/04/2016 at 04:340 Comments

I was the main course. I wish that guy over at the LTCC PCB shop would fix his press!

According to the latest search, circa July 3, 2016, it cost around $1000 to process the human genome with 30X coverage, meaning that there is an error around .1%. So, every 1 out of 1000 base pairs there will be an error. A C should have been a T, a A a G, etc.. Absolutely, of no relevance. Science has only one direction, forward.

So, what exactly does Space Grade mean? When, in a few years, SpaceX lands a crew on Mars, they will leave behind at least one instrument for molecular biology. Thousands of years later, archaeologist rediscover the landing site and find in the sand, half buried, lies a DNA analyser, still functional, that stands as testament to the best engineering principles.

If we are to build instruments that will endure, then we must build them from ceramics as that is the only material that is evidenced to survive the passage of time.

Machines that last. Based upon first principals that endure the passage of time. How does one go about building such machines?

Had this been a journal paper the title would be, "DNA Analysis by Restriction Enzyme Mapping". If you take a DNA molecule and digest it through the application of restriction enzymes, then it will be cut into a collection of smaller fragments. The fragments will be defined by the distance between digestion sites. If the fragments are then electrophoresed, they will be sorted by their molecular size. So, as each fragment passes by a detector, they may be detected, and in the words of Feyman to paraphrase, since I haven't identified the exact quote, "them their electrons that go to the left and those that go to the right". If you can detect it, then you can switch it. And repeat the process. As each chain of nucleotides is digested, producing smaller and smaller chains, the ends of the molecule are defined, until the molecules is of sufficient size to be economically digested via a Sanger process or something like it. The end result is of course a completely sequenced molecule. Run it through again with a different order of restriction to insure correct coverage.

The purpose of this study is to demonstrate that it is possible to detect DNA via relatively simple instrumentation processes. Thus, having demonstrated that detection is possible, the second problem is to do it on an industrial scale. In a simple proof of concept demonstration one might expect to dissipate a few milliwatts of power in moving DNA from point A to B along with detection. This typically would involve electrophoresis voltages of no more than 20 Volts. In an industrial application one should expect to use upwards of 10 KW, with drive voltages of around 10 KV. Huge difference. At an industrial scale the DNA analysis system is now spread out over a large surface, let's say an ice rink. Thousands of slicers and dicers, digesting, sorting, switching DNA in a constant flow with a new genome entering the system every 30 seconds. For an ice rink area the power dissipation could easily be 1 Mega Watt. The use of an ice rink is deliberate. It is necessary, because of Arhenius, to keep chemical processes at a constant temperature, or at least controllable temperature. Running open loop is verboten!

Keep in mind that because the process is running at an extremely high operating voltage in the presence of corona. The detectors, never the less, must detect signals at a nano volt level. Giving the overall system dynamic range of around +160 to +200 dB. No system, to this authors knowledge with this dynamic range presently exists! Further, all the communications processes that exist behind the detector must also be capable of operating at a very high common mode. An yet all of this is possible and practical, based upon a device no larger than a poker chip.

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