Simulate interaction between a DNA and RNA with a Cas9 protein?

Question

[yourgoodnabor]

I was wondering if you can simulate using a certain program or settings, an interaction between DNA and an experimental segment of RNA with a Cas9 enzyme (intended to simulate gene deactivation)?

I really want to be able to simulate this and test out different types of RNA+Cas9 enzyme to see how it deactivates the gene.

Is there a certain program or setting to perform this? Can we use blender/molecular nodes for this?