PCR Short Fragment

[pigfarmer]

Hello,

I was wondering if there is anything I should take into consideration when I am performing a PCR of a smaller fragment (~300bp)? I was actually on vacation, and someone else was doing my PCR for me and all the longer genes PCR worked but the short ones didn't. I haven't had time to do the usual troubleshooting, but was just wondering if there is anything special about such a short PCR?

[Aga]

Actually, taking into consideration Taq polymerase efficiency, PCR amplification of short DNA fragments should cause less problems. Polymerase 'prefers' short fragments.

Similarly, it is more probable that in case of partial template degradation long DNA fragments will be more problematic to amplify, and shorter DNA fragments may still be present in DNA template solution.

There is not enough information to help you in this case, so if you encounter any consistent problems with your amplification give us some additional info.

Good luck