I am working on gene expression. In Real time PCR experiment, a primer dimer is observed.
As the name implies, primers dimerize mainly due to complementarity - either due to self complementarity of a single primer or complementarity due to primers designed for opposite strands. When designing primers choose low values (0-5 bases) for self complementarity or pair complementarity. Also, minimize high GC content at the 3' end of the primer, this stabilizes the primer binding. These steps usually minimize primer dimer formation, but will also minimize the number of primers that are suggested by the software. Other factors can play a part as well, these steps should prevent dimer formation significantly.
http://www.corning.com/uploadedFiles/Lifesciences/PDFs/Axygen_PDFs/Primer-Dimer%20Formation_Problem%20and%20Solution.pdf
Its common to all PCR not specific for Real Time. Reasons may as follows:
1.in correct anealing temperature
2. poor primer design
3. High primer concentration
Try to optimize these parameters if nothing works design a good primer.
All the best
As the name implies, primers dimerize mainly due to complementarity - either due to self complementarity of a single primer or complementarity due to primers designed for opposite strands. When designing primers choose low values (0-5 bases) for self complementarity or pair complementarity. Also, minimize high GC content at the 3' end of the primer, this stabilizes the primer binding. These steps usually minimize primer dimer formation, but will also minimize the number of primers that are suggested by the software. Other factors can play a part as well, these steps should prevent dimer formation significantly.
I endorse answers of subramaniam and Sabarish. Very good Response.
Hi, there was many reasons for that , of course you have to be sure that your primers were good choosen and cheked, i advice you to pick other primers for your PCR, take care about the complementarity of your primers, also about their lenght.
Dear Ramyar Chavoshinejad,
Thank you so much for your valuable opinion .
- Badges
- Science method