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I recently ran a gel on a new system and came out with something I've never seen before.

I loaded the first three wells with a ladder in the first and an uncut plasmid in the next two. There are no bands, just swirls all over the gel.

It's a 10 cm gel, 0.7%, and I ran it at 80 v for 1.5 hours. Part of the new system is the buffer, lithium borate, which I've never worked with before.

Any ideas as to why this is happening?

enter image description here

Edit: thank you for your answers. I followed the regular protocol closely and used the same bottle of buffer for both making and running the gel. I did this twice and got similar results both times.

I had the power supply tested and discovered that the voltage may have been fluctuating between 77 and 83 volts during the run. Could this have caused it?

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  • $\begingroup$ Are you sure you used the right buffers or prepared the correct (dilution, concentration)? $\endgroup$ – Chris Jun 26 '18 at 21:23
  • $\begingroup$ I didn't prepare the plasmid, but I know the ladder is correct. Yes, lithium borate was all it called for, and I diluted it as the instructions said. $\endgroup$ – CDB Jun 26 '18 at 21:29
  • $\begingroup$ What length of DNA fragments are you expecting to see? What is the power (Watts) or current (Amperes) in your region? $\endgroup$ – Tom Kelly Dec 25 '18 at 1:51
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It seems that the gel was not prepared properly and does not have a homogenous texture as it should, which then affects its pores and prevents the sample from traveling through (hence be absence of bands).

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It can possibly be one of two problems:

  1. Either the gel poorly prepared, in that it was cooled for too long, resulting in parts that solidified before pouring it into the mold.

  2. This I have seen before, the pH of the electrophoresis buffer and the buffer used to make the gel was not the same. It has to be the same throughout the gel to ensure that the DNA moves evenly to the positive electrode.

Do you perhaps have a gel image of the bio-transilluminator? It could provide more insight.

Hope this helps

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Electric potential (voltage) should apply equally across the gel. This should not cause DNA to run unevenly. In gel electrophoresis, the electric forces affect all (negatively charged) DNA molecules and the flow in the same direction.

What causes differences in their flow is the resistance to diffusion or flow of DNA molecules by the gel. Larger molecules are more likely to collide with the polymer matrix and will therefore move through the gel more slowly. If you have DNA prepared in varying sizes, they should form well-defined bands. There are several parameters that you can optimise, depending on the sizes of the bands that you want to distinguish:

  • concentration of the gel: a denser gel will slow DNA molecules more and is useful to prevent smaller molecules running off the end of the gel

  • time or voltage: smaller molecules running on a denser gel will take longer to separate so you may need to adjust the running time or voltage accordingly.

It is possible that the gel or input DNA has not been prepared correctly. A gel needs to be mixed and poured while it is still liquid (before it cools) to ensure that the polymer forms evenly. However, the absence of a positive control or DNA ladder even in the wells shows that the DNA is not present in this gel at all: It has run off either end of the gel. Therefore either:

  • the DNA ran through the entire gel: it was run for too long or the polymer was not a high enough concentrate. Prepare a gel with a higher concentration or run it for less time.

  • the DNA ran the wrong way: please check that the electrodes were connected in the correct orientation (negative by the wells and positive at the other end). These should be colour-coded (usually red and black).

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