Summary: Models are great ways to introduce invisible things or abstract concepts, however, models leave out a lot, and can therefore mislead your audience. Best thing you can do is use several models to depict the same thing, then at least your audience can begin to grasp the extent to which different models can vary and see that models are imperfect. And, there are many games that present models of macromolecules like DNA and proteins, so go try them!
Phylo, EteRNA, DNA Damage, Fold It and Transcription Hero all show macromolecules (Proteins, DNA and RNA) as simplified models, but each model is very different. Each model shows different aspects of these biological molecules' functions. I believe that simplifying complex biology by using models can be confusing and misleading. Everyone who uses a model knows this: certainly teaching about the solar system using models in class can be misleading. This is the nature of models. The student does not know what simplifications have been made and without ever seeing another model, the student does not even know to ask about the missing details. Using our solar system analogy, in the in class model, perhaps strings hold of up the planets, this giving the student a confused idea of gravity's effect on the solar system.
I think that models are necessary, because otherwise we can't show the huge solar system or the tiny macromolecules to students at all. Models make teaching possible. No one wants to learn everything about DNA in one sitting anyway: models let us teach one aspect at a time!
One simple solution to these problems of teaching with models is to use more than one model. Simply introducing two models for the same thing can demonstrate to the student that models are imperfect representations, and start to let the student see that each model is missing something they other has... providing the best clue that perhaps the thing being modeled may have characteristics that are not modeled by either model.
So my advice to anyone using a game to teach about macromolecules: Use more than one game! Use several different games about macromolecules to teach kids (and grown ups). Start with Fold It and get a sense of the complexity in macromolecules. Play 10-20 or 50 levels shaking and folding proteins. Then play etRNA and learn about how this complex molecules are actually made out of repeating beads. In etRNA you learn about how different "beads" in this long nucleotide string will interact with each other: a feature present in proteins and modeled in a different way in Fold It.
Has anyone tried these games themselves or with a class? Do you have any thoughts or results to share?