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Problem: VisualDSD internal toehold reaction #9

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the-casle opened this issue Oct 27, 2022 · 0 comments
Open

Problem: VisualDSD internal toehold reaction #9

the-casle opened this issue Oct 27, 2022 · 0 comments

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@the-casle
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I am not sure if VisualDSD can simulate strand displacement when an internal toehold is used to initiate the reaction. The invading strand did not pair with the toehold in this case. This is shown below, where no reaction takes place.
Pasted File

The second picture below shows what I would expect to happen, the only difference being that it is external now. Am I missing a possible directive or is this a bug?

image

I also have Nupack simulations which show that the structure of the complex to the left of the toehold shouldn't affect how the toehold is attached. Below is the code I used in VisualDSD to generate the reactions, where the commented line is the external toehold.

directive simulation {
  final=600; 
  plots=[Backbone();Access()];
}
directive simulator deterministic
directive parameters [k=0.003;u=0.1]
directive compilation detailed
directive polymers

directive rendering {mode = nucleotides}
directive unproductive

dom tag = {bind=k;unbind=u;colour="red"}
dom val0 = {bind=k;unbind=u;colour="green"}
dom val1 = {bind=k;unbind=u;colour="blue"}
//def Backbone() = {cap}<tag^>[reg1]
def Backbone() = [reg0]:<tag^>[reg1]
def Access() = {tag^* reg1*}
( 1 Backbone()
| 1 Access()
)
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