I completed the FMN switch 2.0 with a melting point of 47 degrees. Why is a low melting point bad and how do I control the melting point?
Melt temperature means the temperature where the your lab design will fall apart and be single bases instead of paired up, so it is basically the temperature where the bonds between the basepairs break. Low melt temperature means the bases of your lab design will fall apart at a low temperature, high that it will first fall apart at high temperature. Both things are potentially bad. Eg. usually a design made of only GC-pairs will not work, as the pairings of the basepairs gets too strong and the fold gets stuck in a wrong way. Those typically have a really high melttemperature. And a design with many AU-pairs have too little strength to stick together and fold correct.
You can control melt temperature and make it higher by adding in more GC-pairs in your design. You can lower your melt temperature with adding in more AU-pairs.
Usually when you look at past labs, there seem to be a certain range of melting temperature, that the winning designs are in. Here are the tendencies for the 2 switch labs before the current one:
The Simple RNA switch seemed to do good in a temperature range of 67-87.
The FMN aptamer 2.0 do good in a temperature range between 77-87.
That still might be a bit too narrow range for both of the labs. But it tells you that a melt plot on 47 and 107 is probably a no go.
For the old single shape labs, the melt temperature have been both lower and higher for some labs. What is good depends a bit on the design and it’s type of structure, but generally low and very high temperature is not good.
For more on meltplot, check this: