If a standard polymerase chain reaction (PCR) does not yield the desired amplicon, it may be necessary to troubleshoot steps and optimize the reaction to attain better results. First it is necessary to assess the results. Troubleshooting PCR reactions may be a frustrating endeavor however, careful analysis and a good understanding of the reagents used in the experiment can reduce the amount of time and trials needed to obtain the desired results. In general, the stringency of the reaction should be assessed, as titration of Mg2+ and/or manipulating annealing temperatures can often solve most problems.

Below is a helpful guide in deducing issues, and troubleshooting the correct steps. At large: