User talk:ElNando888/Blog/Designing for the A B lab

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Hi all this is interesting. is there any way you can post this in the lab forums so we can ask questions and discuss all this?

By "lab forums" do you mean GetSat? The main issue there is that I wouldn't be able to post the content because of formatting issues, specifically with the bottom table. Or control whether clicking a picture opens a new tab with the full-size one. Also, anyone can start a discussion on GetSat about this topic. And on GetSat I don't have the possibility of appearing as "just a player", I'm in an "official" position, sort of. Posting the document here is an attempt at emphasizing the fact that I'm speaking on my behalf, not on behalf of the Das Lab.

Finally, since the content is here on the wiki, why not simply ask questions on this discussion page?

ElNando888 (talk) 11:38, 13 October 2015 (UTC)

"the free energy of binding for the MS2 protein does affect the folding of the RNA".  Why is that?

Omei (talk) 18:43, 31 October 2015 (UTC)

When the MS2 coat protein "docks" to the MS2 RNA hairpin, multiple hydrogen bonds are formed, and they contribute a certain amount of free energy to the complex. This factor causes changes in the partition function, since the probabilities for secondary structures containing the MS2 hairpin increase, while conformations without it become less likely by the same amount.

For what it's worth, the binding affinity for MS2 is measured to be Kd = 2.5 nM in the Greenleaf paper. For instance at 100 nM MS2 in the solution, the bonus is about -2.3 Kcal/mol.

In the previous labs, this factor is mitigated by the fact that the lab people were applying "soft measurement" techniques, like slowly increasing MS2 concentrations. And the numerical analyses may have been corrected as well (I don't know any details though). But if everything has been done to nullify the "free energy of the MS2 binding contribution" factor, how come the Same State FMN targets were so much easier to solve compared to the Exclusion ones? When one takes into consideration that the MS2 docking will "help" Same-State type switches, and "impede" Exclusion ones, one may wonder if these factors were actually properly nullified...

Finally, in this next experiment, I don't believe that there will be multiple runs at various MS2 concentrations, which supposedly will reduce the capacity for "soft measurement"...

ElNando888 (talk) 22:06, 31 October 2015 (UTC)

Nando, this probably seemed like an odd question for me to be asking.  I can't figure out why, but I had read your sentence as "... the free energy of binding for the MS2 protein does not affect the folding of the RNA". :-(

Omei (talk) 20:13, 2 November 2015 (UTC)

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