The PCR Simulation is an "inside the box" exploration of how the polymerase chain reaction, or PCR, creates millions of copies of DNA from a single DNA template strand. This is similar to the copying process that occurs in vivo or naturally in dividing cells.

To learn more about the five ingredients used in PCR:

1. Click on "Ingredient Info" icon found on the bottom left of the screen. The icon looks like this:
   
   
   
   
   
2. Once the screen loads, you can click on any of the grayed out ingredient icons on the left to gather additional information about each ingredient.
3. Click "Close" to close this screen and begin.

To use the simulation and begin experimenting with how PCR works:

1. First add the ingredients. To do this, click on any combination of the five ingredient icons found on the left side of the screen. The ingredients are represented by the following icons:
   
   
   
   
   
2. Then click "Start" (found in the upper right hand corner of the screen).

Add different combinations of the ingredients to your mix to see how the ingredients react with one another. For example, can you run the simulation with some but not all the ingredients? Which ones?

To clear your screen and start over at any point, click "Reset."

The "Help" button is available at any time and will open instructions for running the simulation.

To perform the steps of PCR

Once you have selected and added ingredients to the mix, you can run through the cycles and steps of PCR. Notice that the temperature changes as you go through the steps.

1. Once you click the "Start" button, a temperature gauge will appear in the bottom right corner of the screen.
2. Click on the "Denature" button on this temperature gauge to heat the DNA to just below the boiling point. Denaturing breaks the chemical bonds between the two strands and the DNA splits down the middle.
3. Next, click "Anneal" to cool the mix, and the primers anneal to the original DNA strand.
4. Then, click "Extend" to see how the DNA polymerase extends both primers and both strands are successfully copied.

After one cycle:

1. Click "Reaction Info" located in the bottom left corner to find out what happened in your test.
2. You can run the reaction multiple times if there are available ingredients. Run the reaction again by clicking on "Denature", then "Anneal", then "Extend."
3. When you are ready to start your test over, with new ingredients, click the "Reset" button.