Here is the analysis:
Here is the discussion:
The switch was designed in Nupack.
The requirements I think about in addition to the puzzle requirements are:
1.) I would like to see each aptamer break apart as much as possible between off and on states and
2.) Minimize the distance NTs have to travel between the on and off states to create the switch.
You can break the switch sequence into 5 parts. A top stem, the spinach aptamer, a folding area ( for lack of better terminology ), the molecule aptamer and a closing stem.
I control the switch from state 1 to 2 by manipulating the folding are. The folding area can be either passive or aggressive. An aggressive folding area either creates a slide between NTs or targets a portion of either aptamer.
Some of the more positive attributes to the design are that:
1.) State energies are very close, switch doesn’t have to have some sort of energy boost to move from state 1 configuration the state 2.
2.) Arc plot X factor levels are balanced and high giving the same probability for closure on either side of the spinach aptamer.
3.) One side of the spinach aptamer binds to the molecule aptamer in the off state.
4.) Valid in all 3 engines, ( do not know if this is important ).
5.) Both aptamers are completely broken apart in the off state
6.) The distance NTs have to travel to its associated pair in the next state is acceptably minimized.
This particular design uses a passive approach, which means the folding area plays a subordinate role in the sequence. The folding area is made up of predominately AUs and only bind in one of the states.
So where does the sequence get its initial momentum to switch between off and on?
I would say it is the initial stem built with strong GCs and immediately connected to the spinach aptamer that does the trick.The sequence of events might be something like: The folding of the strong initial stem pulls the half of the spinach aptamer away from its attachment to the molecule aptamer to allow the molecule to close it’s aptamer.