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FAQ for "A Magnetic Primer Designer"

Postby amyc » Thu Sep 20, 2012 3:43 pm

The following FAQ contains frequently asked questions and answers about the "A Magnetic Primer Designer" Project Idea and/or Project Kit ( If you are having trouble with the procedure, you may find assistance in the answers below.

Q: Why should I test at least seven different primers, in addition to the controls?
A: You will get better results when testing seven different primers compared to testing fewer primers. Testing seven different primers should let you easily see a trend in your results. Do not forget that you can re-use a primer as a different primer by flipping it over!

Q: Why do I need to test each primer three times (in three trials)?
A: Testing each primer at least three times will help you make sure that your results are repeatable and reproducible. You may actually notice a little variation in the amount of pennies needed to make the primer fall off when testing a given primer three different times, which is why you will use the average of your results when making a graph.

Q: Which side of the magnet is the plus (+) and which is the minus (-)?
A: Remember opposite poles attract and like poles repel! In this science project, it does not really matter which side of the magnet you label "plus" and which you label "minus" as long as you are consistent; when you push poles together with the same label (they are both plus or both minus), the magnets should repel each other, whereas when you push poles together that have different labels (one is plus and one is minus), the magnets should be attracted to each other. By stacking the magnets and marking the same side of each magnet in the stack (such as the top side of each magnet), you are labeling the same pole on each magnet. (You arbitrarily call this the "plus" side in this project.) Some magnets also come dimpled where the plus side is located. Some magnets do not have a clear plus and minus side, and may seem to attract each other no matter which sides are interacting. For this project you need to use magnets that have a clear plus and minus side.

Q: I added 60 pennies to the cup, but the primer strand did not fall off of the DNA template strand. What should I do?
A: If this happens when you are testing strands with 5 matches (0 mismatches), but this does not happen when you are testing strands with 4 matches (1 mismatch), then five bonds between your magnets may be just a little too strong to break using 60 pennies. There are multiple things you can try in this situation. If you have more pennies, you can try adding more until the primer falls off. Alternatively, you could write "more than 60" for the number of pennies needed in this trial. If you are using the kit that goes with this Project Idea, the magnets should be weak enough that about 60 pennies at most are needed to break five bonds. If this happens when you are testing strands with 4 or fewer matches (1 or more mismatches), the magnets you are using may be too strong to do the project as written. In this case, we suggest cutting a strip of felt that can be placed between the two strands and testing all of the primers with this strip of felt placed between them and the DNA template strand. Alternatively, you could use smaller and/or weaker magnets.

Q: It seemed like I needed to add more pennies to make the primer strand fall off when there were 4 mismatches than I needed to make it fall off when there were only 3 mismatches. Why would this be?
A: When you pair the primer strand up with the DNA template strand, make sure that the primer strand is not flipping over on itself and creating more than 1 match with the DNA template strand (or the primer strand). Because magnets like to bond with each other, the primer strand will try to find ways to create extra matches with the DNA template strand (and the primer strand). The primer strand should be hanging flat against the DNA template strand.

Q: I marked one side of all of the magnets, but my markings came off! What should I do?
A: If you stack the magnets or put them in the tape before the paint pen markings are completely dry, the markings can come off. Re-mark the same sides using the paint pen and be sure to let the paint completely dry before using the magnets.

If you have other questions about the procedure or need assistance troubleshooting the "A Magnetic Primer Designer" Project Idea and/or project kit, please post your question in the forum at Ask an Expert: Our team of volunteer Experts is available to assist. We attempt to reply to questions within 24 hours. Please note that you will need a free Ask an Expert account in order to post questions.

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