Biomod/2011/UTAustin/Hook'em Hybridizers:Tools
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Tools
Few systems work the first time they are built, and a nanoscale molecular machine is no different. Given that the kinetics of DNA interactions are well studied, we proposed that it should be possible to simulate our counter system computationally. A number of important questions can be answered about our system using simulation. For example, we could ask what the optimal concentrations of threshold strands and gate strands are to ensure that our machine functions.
There exist software tools for simulating nucleic acid systems. Notably, Nupack and Visual DSD are both good options for many system applications. However, neither was able to completely simulate our system adequately. Hence, we developed TripleSim.
TripleSim is a
- unpSeuddoknotted
- Secondary
- Structures
- Simulator
Like Visual DSD, TripleSim uses dynamic compilation to discover the "most important" reaction pathways through a system (diagram, below). Even though DNA has been shown to undergo only three main reaction types (figure below diagram), there are still an exponential number of reaction pathways that nucleic acid reagents can follow. Many of these "possible" reaction pathways are highly kinetically disfavored- a computer program which removes highly disfavored reaction pathways would be useful from an analysis perspective. Hence, TripleSim attempts to produce a reaction network representative of the behavior of a nucleic acid system, with off-the-main-road side products shown (graph, second to bottom). The most favored reaction pathway from the input signal to the output in our counter system is a subgraph of the reaction network produced by TripleSim (graph, bottom).
(Node numberings correspond to distinct reaction species, not shown).
