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I am currently working on my masters degree and have recieved the following question:
"you want to amplify by PCR a gene 1kb long. The Taq Polymerase you have in the lab is able to synthesize 1kb/minute. You make a mistake in programming the PCR machine and set the extension time to 30 seconds instead of 1 minute. what will happen? what do you expect to see on a gel?"
The answer I came up with was that there would be insufficient time for complete replication of the target and therefore only incomplete copies would be made. These strands would show up in a band below 1 kb because the are shorter. This answer however, was incorrect. I browsed the web but could not find any clear answers on what would happen. anyone knows what happens?
To get amplification of a DNA fragment you need primers to anneal first so that you can extend from. The extension time is designed so that DNA is synthesized from one priming site to the other. Therefore if you have a lower extension time you will make a product that is missing the other priming site. This means that all new template strands can be amplified from one end only and you get linear amplification, not exponential. Therefore there will be too little DNA to visualize on a gel.