Intro
This strategy is courtesy to jandersonlee and based on his superior round 1 microRNA design strategy, that ended hitting through among the majority of the winners in the following round too.
Strategy for microRNA labs
I wish to reward when there are a series of dangling single bases in the unbound state, that are complementary to the early part of the microRNA.
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Give +2 for each complementary base in the dangle that are capable of pairing up with the first 8 bases of the MicroRNA (counting from 5’ end)
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Give -1 if one of these bases are not the strongest complement.
General MicroRNA dangle ranking
Best position of the dangle ranged in order of best to worst:
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MicroRNA complementary series of bases is in the 3’ end of the RNA design in an dangling tail - Give full points of the sum of the above
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MicroRNA complementary series of bases is in gap bases - stretch between elements - Give 3/4 points of the sum
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5’ end of the RNA design in a dangling tail - Give 1/2 of the sum
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Multiloop ring bases - Give 1/3 points of the sum
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Give 1/4 of the points for the design that has a dangle that aims for anything else than the first 8 bases of the microRNA.
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No dangle - no points 
Background articles
MicroRNA welcoming dangling tail
Imagining the microRNA labs
1 Like
Dear Eli Fisker,
Your strategy has been added to our implementation queue and we should have it completed within the next two to three weeks. You can check the status of the implementation here.
We will also be uploading the code used to write your strategy on this page if you are interested in reading it later.
After implementing your idea, we will post the direct link to the code here. Then, we will then optimize the parameters, and test it. At that point, we will tell you the correlation of how good your strategy was and what the new optimized parameters are.
Thanks for sharing your idea!
Vineet Kosaraju
The EteRNA Team
Hi Eli,
I have a question about the strategy, about the ordering of dangles.
The very best one is where the “MicroRNA complementary series of bases is in the 3’ end of the RNA design in an dangling tail” - I understand this
The next best one is “MicroRNA complementary series of bases is in gap bases - stretch between elements” - can you show a screenshot? I’m confused what the gap bases are
The next one is “5’ end of the RNA design in a dangling tail” - I understand this
Multiloop ring bases - will these be the ones highlighted in this picture? Can you show a screenshot as well?
Thanks,
Vineet
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Hi Vineet!
Here are some answers back on your questions.
Gap bases explained
Here is what I understand with gap bases. I define gap bases as any kind of single base/s stretch that are single bases between two RNA designs elements, and where the “ring” they participate in is not a multiloop. Since both the tails of this RNA sequence are dangling, the 4 base stretch between the main section and the barcode is gap bases. Now I wonder if they have a correct scientific term.
I don’t count single base/s in bulges or between internal loops. I simply count gap base/s, when the base/s are between elements in the hook section.
Multiloop ring bases explained
I borrowed your picture and added in orange the multiloop ring bases. With multiloop ring bases, I simply mean all the bases that are between the stems in the multiloop.
Dear Eli Fisker,
I am pleased to announce that a preliminary version of your strategy has been implemented with 58 lines of code. The code might slightly change in the future to remove bugs, but you can check the current version here. We will soon work on optimizing your parameters and testing the strategy.
Thank you again for sharing your switch strategy!
Vineet Kosaraju
The EteRNA Team
