SNaPshot™ Primer Focus™ Kit - FAQs

The extra peaks could be due to incomplete removal of PCR primers, incomplete removal of dNTPs from the PCR reaction, or incomplete removal of the fluorescently labeled ddNTPS from the SNaPshot reaction. Residual PCR primers and dNTPs will both participate in the SNaPshot reaction. For the PCR purification, please use fresh SAP and Exo1 or use another method of PCR purification. To address incomplete removal of fluorescently labeled ddNTPS, use fresh CIP or SAP.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

Due to the influence of the dye on the mobility shift of the DNA fragments, the reported sizes will differ by a few bases from the actual sizes. This is particularly true with the shorter fragments as the relative contribution of the dye is greater. It is also recommended that you have a tail on the primer with a 5-7 bp difference between them to further separate the samples so there is no overlap.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

This is normal as the SNaPshot control shown in the manual is from a 3100 Genetic Analyzer and POP-4 polymer. Dye-labeled DNA fragments can yield different sizes when run with a different instrument, polymer type, capillary array length, or size standard. Although the control sizes may not match that in the protocol, once the size has been established, the precision, or reproducibility will be consistent for a given fragment.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.