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I have an idea that you could find out which substances are within a sample in vitro that you are investigating by creating DNA that has a bunch of different promotors for different substances you are interested in.

After inserting those DNA strains you could do nucleotide sequencing and as nucleotide sequencing allows you to to read a lot of data you could read the sequencing behind the promotors.

How complicated would it be to build DNA with promotors for dozens of medically relevant substances?

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  • $\begingroup$ 1) What do you mean by within a "probe"? Do you mean "sample"? 2) Are you thinking of these detector DNA molecules as being within an organism or in vitro? 3) Also note that typically when this type of experiment is done we would look at protein readouts since proteins can be fluorescent or have enzymatic activities that are easily measured. Is there some reason you want to do a sequencing based measurement and if so why do you think that would be preferable to just doing a standard test e.g. one based on antibodies? $\endgroup$ – tyersome Jan 1 at 1:10
  • $\begingroup$ @tyersome : I mean in vitro. You can't measure dozens or hundreds of different fluorescent proteins at the same time on the other hand if you have working promotors you could detect many targets at the same time. The cost of antibody based detection has stayed relatively constant over the last decades while nucleotide sequencing is a technique that fell a lot in price and there's hope of further price drops even if it doesn't fall faster then Moore's law anymore. $\endgroup$ – Christian Jan 1 at 11:56
  • $\begingroup$ Dozens of fluorescent proteins might be possible, but I agree hundreds would be right out. —— I don't want to be a wet blanket, but are you familiar with what transcription involves? Transcription requires multiple components — doing this in vitro would require a mixture including: DNA, transcription factors§, RNA polymerase, and ribonucleotides. All of these macromolecules are subject to degradation and would typically be stored separately at -20°C before mixing. ——— §Note: For each hormone you would need a specific transcription factor that respond to that hormone and bound one promoter. $\endgroup$ – tyersome Jan 3 at 0:54
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Promoters bind transcription factors (TFs) and RNA polymerase (or a related complex, in the case of eukaryotes).

The substances you are interested in testing would need to bind to DNA in the same way as TFs and RNA polymerase, in order to trigger RNA synthesis (which you might measure with RNA-seq experiments). That would seem to severely limit what you can test the presence of.

In any case, if you could make that happen for your substances of interest, you would probably also want to make sure to avoid degradation effects of short-length RNA, by removing associated proteins.

https://en.m.wikipedia.org/wiki/Promoter_(genetics)

https://en.m.wikipedia.org/wiki/RNA-Seq

https://en.m.wikipedia.org/wiki/Small_RNA

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