A Guide to Loop Boosting
An EteRNA Guides Production
Boosting Defined
Internal Loops
Internal loops are Closed loops (red highlight), with a stack closing it (light blue highlight) on both sides.
Boosting an internal loop
Free energy of internal loop = 2.3 kcal
Free energy of internal loop boosted = 0.1 kcal
Boosting an internal loop
As you can see, when boosted, the free energy of the loop on the right is lower, which is GOOD!
Lower Free energy is better.
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How to Boost?
What do I do?
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How to Boost?
Boosting occurs when there is a G-A mismatch in the loop on the bases next to the stack
How to Boost?
Closing Base pairs of Loop - Highlighted Blue
Bases next to closing base pair - Highlighted Red
Free Energy - Highlighted Green
How to Boost?
The G's (circled by Yellow) across from the A's has lowered the free energy to 0.1!
How to Boost?
The G's (circled by Yellow) across from other G's DOES NOT lower the free energy of the loop - NOT GOOD!
How to Boost?
Even though we have G across from A, they are not next to the closing base pair, and this does not lower the energy in the loop. NOT GOOD!
How to Boost Conclusion
What have we learned?
Types of Internal Loops
Type 1 Internal Loop - Sym/Asym
Type 2 - 1-X Asym Loop
Type 3 - Bulge Internal Loop, 0-X
Special Loop Circumstances
There are special circumstances and sequences for certain loops. These sequences will not always follow the rules previously described in this presentation, but these sequences will also not apply to any of the previous loop types already stated, being specific to the type of loop.
These loops are the 1-1, 2-2, and 1-2 loop
Special Loop: 1-1 Loop
As stated previously, G-A mismatches are the best in a loop.
Free Energy = -0.1
However, in 1-1 loops, G-G mismatches are the best.
Free energy = -1.7
WAY BETTER
Special Loop: 1-1 Loop
So, as a general rule. When you see a 1-1 loop, which is a loop with one free base on each side, use G on both sides for the lowest possible free energy.
Special Loop: 1-2 Loop
Much like the 1-1 loop, the 1-2 loop can be boosted by a G-G mismatch. On the next page, are some of the better boost options for the 1-2 loop.
A 1-2 Loop is a loop that has 1 free base on one side and 2 free bases on the opposite side.
1-2 Loop
Each of these are valid boosts
The 2 G's across from the A is typically the best.
Special Loop: 2-2 Loop
A 2-2 loop is a loop that has 2 bases on each side of the loop
Can be boosted just like any other loop for a bonus in free energy.
This is not the best way to lower the energy (Under most circumstances)
Special Loop: 2-2 Loop
This is the best way to lower free energy in the 2-2 loop, the tandem UG mismatch
When viewing the numbering of the bases on the RNA, going from lowest to highest, the lowest number must be U, and the highest G.
What happens when you reverse the orientation of the G's and U's?
Special Loop: 2-2 Loop
As you can see, reversing the orientation of the bases in the loop raises the energy WAY up. This is bad, real bad. Remember, we want the energy in the loop more negative, or lower, and reversing the bases does not do this.
Thank you for taking your time to watch this presentation, may it have helped in your journey to better your skills in EteRNA.