weird PCR ask for help - (Jan/17/2010 )

Hi there, has anyone here encountered this problem: I did three batches of pcr last Monday and Tuesday. Target bands showed in gel. But when I run my latest PCR products (last Thursday and Friday), pcr product seems to get stuck in the well. I use the exactly same program and reaction system which worked before. I thought it may be the problem of reagents and I changed new tubes of buffer, dntp, primers and taq. It didn't work. I even used the exactly same templates which worked in Monday and Tuesday and the result are same. No target bands at all and products stay in gel wells. The taq i use is only 0.15ul vs 25ul. So it could not be the reason of excessive taq. what could be the reason? Thanks very much.
The attached is gel picutre. The left side are the targe bands (are boxed; 160bp) and the right side is latest gel result.

It could be your gel. Sometimes if you don't clean out the wells of the gel, your DNA won't run properly due to obstructions in the gel itself. I would make another gel, wet it in the running buffer, then aspirate up and down with a pipette tip each well to clean it out. This way you are sure not to have obstructions. Or buy a pre-cast gel and run your material, and use that to compare. I bet it will run down as normal as before.

what do u kindly mean by this ?

have you tried diluting the samples ?

claritylight on Jan 17 2010, 01:41 PM said:

Thank you. i just have a question: if the problem is gel, why the marker can run down normally? The gel in picture was not the only one which had the problem. I run four gels last week. All the result were same but the marker was ok.

nightingale on Jan 17 2010, 02:00 PM said:

Thanks for your response. I doubted it could be the problem of template cause I had already changed all other reagents (dntp,primer,buffer and taq). So I tried the samples which I got bands before. To see if I can get bands or not. If yes, the problem is the templates I used later. But the answer is no. I got nothing with the templates that I used before.

I don't do this yet but the concentration of samples is not high.

Frankly, it does looks weird to me.
Just want to find out, what is your agarose gel percentage? Sometimes when increase the taq concentration, you will get a very high band (but very less likely you encounter it).
Make sure you are running your gel in your running buffer than pure water. Another possibility is might be your gel loading dye. I guess there might be something there which "stuck" your DNA there (too much glycerol??).

I really got no idea... just to voice out the thought from my mind and see whether it could help you in any way...
Adrian

adrian kohsf on Jan 17 2010, 06:11 PM said:

Thanks Adrian. I use 1% agarose gel to run product. I'm running buffer not water cause the marker run down normally. So does loading dye.

nccutudou on Jan 17 2010, 04:40 PM said:

This is weird indeed.

I want to make sure I understand. You took the PCR product from Monday/Tuesday, re-ran it on Thur and had DNA stuck in wells when before it had migrated?
Are you saying that the exact same PCR product is running differentely?
What's the size of the amplicon? Couldn't it be that last week was the weird gel?

u r most welcome

are you saying that :-
u ran 2 PCRs for the same samples, the first gave bands while the other no ????

have you used the same cycler ?

nightingale on Jan 18 2010, 09:55 AM said:

Thanks for your kindness, nightingale.

Yes, that's what I mean.

I've tried both same and different cyclers (Eppendorf Mastercycler Thermal Cycler). They gave same results.