Can I use other fluorophores instead of SYBR Green?

The performance of the PCR Add-on and Reamplification Kit V2 was extensively validated with the SYBR Green I nucleic acid dyes listed in the User Guide (Sigma Aldrich, S9430; ThermoFisher S7563).

We do not recommend the use of qPCR master mixes or alternative fluorophores (e.g., EvaGreen) as their performance can vary and influence calculation of the endpoint cycle number. If other fluorophores are utilized, the endpoint cycle numbers may need to be calculated differently and verified by Endpoint PCR testing prior the library amplification.