Tuesday, October 28, 2008

Now you see, now you don't

I got my intended product bands last week. I was so happy, I thought I have found out the reason that caused my misery. So yesterday, I did everything the same as last PCR, thinking that i should be able to generate some data for analysis. So, I run my PCR, then prepared my gel, then run the gel, and waited. And turned out to be that there isn't anything on the gel except the DNA marker. I scratched my head not understanding why this "now you see, now you don't" phenomena keeps happening to me.

So I tried to troubleshoot:

Buffer problems hypothesis.
-but then I used new buffer and MgCl2 last PCR and I managed to get my bands (that's why I thought i found out the reason)

Bad dNTPs hypothesis.
Background: The nucleotide triphosphates (dNTPs) are probably the least stable component. One should have the 10X dNTPs distributed into small tubes (e.g. 200 ul) that are kept frozen, used a few times each, and then discarded.
Symptoms: - i) The same tube of dNTPs has been repeatedly thawed and used for weeks. - ii) A new batch of dNTPs was just made up. Tests: Try a new tube of 10X dNTPs in a side by side comparison with your old tube.
-but then I have just changed my dNTPs! And they are commercially available!

Anyway, I'll try this out today to eliminate this possibility. If still the PCR give me no bands, then i think it should be

Bad karma hypothesis.
Background: This is basically the "God is punishing you" hypothesis. It sometimes gains a great deal of favor.
Symptoms: - i) All rational explanations have been exhausted and yet PCR still is not working for you. - ii) Persistent feelings of guilt (if you are a Catholic, this symptom could be misleading).
Tests and solutions: - i) Try bungee jumping. If you survive, God must not be too hacked-off at you. - ii) Atone for your sins and start over at the top of the flow chart. - iii) If you end up here next time, have someone watch you next time you set up your PCR reactions.

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