I will like to ask for a strategy for static labs, that has similarities to my earlier strategy Catalog of necks. I believe that good aptamers can be recycled just as can good necks. I am asking for a big broad strategy that says:
Reuse perfect aptamers and near perfect from earlier designs (be the aptamer FMN, Theophylline or whatever). I will like the aptamer cut out, so it has two basepairs to both sides with it, from the design it originated in. This is cut just like in Mat’s Lab Design strategy.
And I will like these good aptamers ranked like I can get them ranked in Mat’s and Jnicol’s CSE tool. Then the strategy should pick what aptamer will fit best for designs with a similar length of stems on both sides of the aptamer. This strategy rely heavily on Mats lab designing ideas. This strategy is as much his as mine.
For more about the thoughts on interchangeable aptamers, read here.
Hmmm. An interesting idea. However, when Tom talks about a perfect aptamer, he is referring to the SHAPE and DMS data after the FMN molecule has been introduced to the RNA. Before the FMN molecule is introduced to the solution, the ligand binding site could potentially fold into any number of conformations, each just as valid as the others. Now, if the SHAPE data we get for these labs like FMN Binding Shapes is the data *after* the molecule has been introduced to the solution, then yes, your strategy could very well be valid. If not, I would see it as more of potential strategy for switch labs, with specific sequences that could aid in the binding of the molecule, by making the correct fold more likely to happen.
Brourd got me wondering if single shape labs were really tested for how well the aptamer bound to the FMN molecule, just like the switch labs, I asked Tom. Here is the answer he gave:
Just to let you know, I made sure that all of the cloud lab RNAs were together probed with FMN. The FMN aptamer is still capable of binding FMN even when it is not in the switch. Also, the nucleotides in the aptamer should have the same reactivities in the presence of FMN, regardless of whether or not they are in a “static” shape or as part of a switch. The exception to this is if the switch is not switching all the way!
Another important point to remember is that FMN should only have an effect on RNAs that contain the FMN aptamer. Non-aptamer nucleotides and RNAs without the aptamer should not be affected by the presence of FMN. This fact is important for our new RNA chemical probing strategy, where we probe many more RNAs at once in a single tube!
