Detailed Protocol for Initial Experiment  

Below is one version of the protocol for our initial experiment. The goal of this experiment, as discussed earlier (see this section), is to test the simulator's theoretical predictions regarding the ability of oligonucleotides having different numbers of mismatches to serve as primers at several different temperatures. This information will be used to calibrate our model, if needed. Additionally, performing this experiment gives us practice in basic labortory techniques that will be needed in the later experiments involving actual DNA machines.