Re: [DIYbio] Re: A hypothetical protocol for DIYBIO DNA synthesis

sorry just to be clear your going to use a lab on a chip to perform TdT reactions, purify out single nucleotide addition oligos, transfect them into e coli, extract them from e coli and repeat the whole process several times? Ok I won't say this is impossible but to construct such a lab on a chip would be a good deal harder than even doing something as ambitious as building your own surface plasmon resonance imager. Also wouldn't it be far easier to use basic PCR than e coli to amplify the sequence.

actually I did a mathematical analysis based on modelling TdT reactions as a system of ODEs and the theoretical maximum efficiency is 100*e^-1% for one nucleotide additions which is approximately 36.7879%.

On Sunday, July 17, 2016 at 12:01:37 AM UTC+1, Nathan McCorkle wrote:

On Jul 16, 2016 12:39 PM, "CodeWarrior" <code.w...@gmail.com> wrote:
>
> Ah that's workable for supper short >sequences but the yield will be low and >the needed input masive. Imagine you >tune your TdT reaction perfectly and get >a 30% yield of single nucliotide aditions

30% sounds far from perfect... wouldn't perfect be 100%? Also why do you assume 30% when phosphoramidite chemistry is close to 99% already, and we know enzymes work and don't have similar error issues, less stringent  chemistry (enzymes are all water based, phosphoramidite synthesis hates water).

> (which I expect is optimistic). Then let's >argue your seperation procedure is >100% lossless (highly unlikely). After 8 >rounds you'll have less than 0.007% of >the oligos you started with. You've also >had to do 8 seperation a probably 8 >consecutive PAGE procedures.

Oh, i am talking about nanofluidic channels, where you don't need gel or anything more than maybe counter-ion buffers.

>It's just not efficient to add 8 nucliotides >to a sequence. After that you need to >jam a primer on the end and do some >PCR or you'll be working with a sample >diluted out of existence.

Meh, just shove the at-least single molecule into an e.coli with electroporation... 'low' yield 'problem' solved. Seems a boon to me to be able to require at minimum a single molecule of output. Also, I am talking lab-on-a-chip tech, not garage-scale reaction apparatus.