I made my ligations using pGEM-T easy vector system I, I normally used PCR products (product for TA cloning-Taq DNA polymerase and Control Insert DNA (promega like a ligation control) for the transformation I used uncut plasmid like I control. But after I have plated bacteria and left them in 37C incubator overnight I do not have colonies just find circular water bubble in my LB agar with amp (PCR products and Control Insert DNA) but in my transformation control I have colonies. this demostrated that transformation process is fine and my cells are competent. Is possible that reagents of this lot it is degraded? T4 enzyme for example. I repeat many times following the insert kit protocol, What is causing these water bubbles?. When I prepared my plates with LB media I avoid the bubbles all the time.
Those are just air bubbles. Trapped/dissolved air in the media expands when heated at 37C.
Kyle Skalenko is correct that those are just air bubbles in the agar and should have no effect at all. If you let them plates dry a few days before using you are likely to reduce the number of air bubbles and wet spots on the plates. But they are nothing to worry about.
As pointed out, those are just air bubbles and are not going to affect your transformation efficacy. As your control plate has colonies, the problem is in your ligation. It's possible that the reagents of this lot is degraded. You can supplement 1mM ATP and 10mM MgCl2 in your ligation mixture and perform ligation, followed by transformation.
Hi Patricia Barrera ! I am having the same problem as you. No matter I transform ligation or site-directed mutagenesis or even a simple transformation of a plasmid. We are searching what can cause that and what is working for us is: to prepare the LB medium (not use the commercial preparation), being careful to adjust the pH, using water with certified good quality and also the plates. Sometimes it looks like the cheaper the plate, more bubbles.
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