mvresearch

For the last couple of days I have been working on couple of things. Here is a short list:


1) Exciting riboswitch experiments.

I have been testing sxy RNA for ligand binding by adding different ligands and then doing nuclease probing by RNase A to check if a conformational change will happen. Since I was not sure if the RNase assay will work due to the change of reaction conditions (from my regular nuclease conditions), I initially tried it just by adding three different amounts of adenine (as ligand). The gels that I ran gave really interesting results.
First, they confirmed that RNases can happily work in almost any conditions and second, the cleavage pattern was different when the different concentration of ligand was applied. However, I am not 100% convinced that this is simply a reaction to ligand addition: the samples with same adenine concentrations partially digested with different enzyme amounts gave a bit altered pattern.
I repeated the experiment testing for binding of xantine, guanine and hypoxantine, then ran the samples in a gel. The results showed the effect on ligand addition is present in samples that had either guanine or hypoxantine added Cleavage pattern for xantine was same for all of the tested concentrations.
To test if this is a ligand_binding_ effect only, I repeated the experiment with adding different adenine concentrations. If the assay is good I expect to get the same result as for the first trial when the same conditions were applied. I ran a gel with this samples on Wednesday and I'll get the results tomorrow.

I am planning to repeat the experiments using same ligands but different enzyme (RNase TI) to check if the effect will be the same when the same amounts of ligand is added.


2) Thesis writing.

Ok, I started panicking about my writing, so that is why I spent most of the time this week in the office, typing. Today I finally finished the first draft of my Methods and Results section. I am sure that there still going to be lots of work to polish this portion up but I think that this is a good start.


3) Racking tips and media making.

....Officially, I started having dreams about tip racking...
I usually don't mind doing the lab staff, I think, however, that the tip racking is the most boring of all lab activities.