This question is about Lab201 Bulged Star. Is there a reason that the team chose to use the exact same shape for each of the four “arms” ?
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We thought different shapes for different arms might be too much challenge at once - bulges in each arm is making the puzzle hard enough : )
EteRNA team
Hi Jeehyung,
I think that different arms would result in a shape that is much easier to design. But I was thinking of simpler arm shapes, not more complex. For example, fewer bulges. Or simply adding one additional base pair to a few of the stacks to vary the lengths of the arms.
Then the variegation that is needed to result in a stable design would come from both the basic shape as well as selection/pattern of nucleotides.
Just curious, no complaints.
Thanks for your answer.
As a matter of pure speculation, I suspect the identical arms are actually going to make things more difficult because the loops and bulges are all free to interact with each other at exactly the same positions. . . . we already saw some counterintuitive results in the last round that I think point in that direction, can’t wait to see what happens this round. . . .
Hi Alan,
Thanks for your response. I think that I understand what you have described. The loops and bulges are at the same distance from the center point of the closed loop. Their proximity to each other increases the probability of cross-interactions. So using the optimal nucleotide configurations to create the loops and bulges may in reality lead to the formation of “hot zones”!
Yes, this specific shape is very interesting, I’ll have to try to think about what it could look like in 3D.