This tool will calculates GC percentage, molecular weight, melting temperature (Tm), thermodynamics, and all possible primer dimers and hairpins of a single oligo.
After many gels that looked like the picture above, with only primer dimers, we had to reconsider our approach to PCR.
Software Online Tools. - Check for primer dimers or hairpins. Any annealing between your primer pair or of one primer to itself will drastically affect the efficiency of your PCR reaction.
Primer3: WWW primer tool (University of Massachusetts Medical School, U.S.A.) – This site has a very powerful PCR primer design program permitting one considerable control over the nature of the primers, including size of product.
The specificity of fluorescent reporter probes also prevents interference of measurements caused by primer dimers, which are undesirable potential by-products in PCR.
Primer dimers, self-dimer and for alternative to Watson-Crick base pairing, like wobble base pairs or G/C-quadruplexes detection
However, the use of SYBR-Green lacks any specificity with regard to the template, which is to be investigated (that is, the DNA binding site), because the primer dimers, which are formed during the reaction.
analysis, annealing temperature, designing pcr primers, dnasis, gc content, hairpins, lab notebook, melting temperature, Nucleotide, oligonucleotide primers, Primer, primer design, primer design tools, primer dimers,
2 Primer design. An excellent and fast way to select primers is with the free online-tool Primer3, currently in v0.3. Primer3Plus, a variation of Primer3 has qPCR settings. Or just apply the following or similar settings to Primer3:
Primer Design for PCR: Primer guidelines page offers a look at the general and useful guidelines laid for designing primers for PCR reaction including Primer Tm considerations, PCR primer cross dimer values, annealing temperature.