Are there any special PCR parameter requirements when using a biotinylated primer?
We recommend biotinylating the primer on the 5' terminus to avoid interfering with the extension of the nacent strand. As long as the biotin is properly placed at the 5’ terminus, the modification is not expected to affect the properties of your primer. A biotinylated primer can be used under the same reaction conditions that would be used in an unmodified oligo. If you do have trouble getting an efficient reaction, a Mg2+ and/or annealing temperature optimization process can lead to more efficient amplification.