Learning through failure

Someone, I don’t remember who, told me that those days when nothing seems to work are not wasted; in fact, you just learnt several ways how not to solve the problem.

Today was the perfect example. I’m trying to make a piece of DNA of a certain shape and size. This involves ligating (sticking) two different parts of DNA together. To test if things have stuck together we place the DNA in an electric field and ‘run’ it through an agarose gel. Different sizes and shapes travel faster than others enabling us to see if the sticking worked and also to cut out the bit we want.

I was successful in sticking together the DNA I wanted, as you can see in the first image.

The red arrow points to the band (or DNA construct I want). It is the brightest in that particular column (lane).

All good so far.

Now I wanted to shove loads of the same DNA through the same type of agarose gel. In this way I can cut out the band of DNA I want and leave all the rest behind.

Following the same protocol as before I now ended up with the second image;

The red circle shows the weird smearing — not that it needs to be indicated because it’s so horrendous!

A massive smear where my distinct band should be!

Why? Why is this? I’ve run this experiment before and it worked great. Indeed the test gel above showed the bands I wanted. For some reason the bands have become smeared!

Any ideas as to why are, of course, welcome!

This is incredibly frustrating but in the long term this will be a positive; I will have learnt another way not to do it.

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