Mike Barnkob:Protocols/Cloning/Primer Design

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Primer design

General notes and guidelines on primer design.

Notes

General:

1. Primer length: Between 18-25 bp
2. Melting temperature, Tm: 52-58°C
3. GC Content: Between 40-60%.
4. GC Clamp: The presence of G or C bases within the last five bases from the 3' end of primers (GC clamp) helps promote specific binding at the 3' end due to the stronger bonding of G and C bases. More than 3 G's or C's should be avoided in the last 5 bases at the 3' end of the primer.

Websites:

1. PrimerBank
2. Primer3web

Check:

1. Secondary structures: Check for hairpins, self-dimers and cross-dimers at OligoAnalyzer
   Hair-pins: Larger negative value for ΔG indicates stable, undesirable hairpins.
   Self-dimers: A 3' end self dimer with a ΔG of -5 kcal/mol and an internal self dimer with a ΔG of -6 kcal/mol is tolerated generally.
   Cross-dimers: Interaction between sense and antisense primers, where they are homologous. Optimally a 3' end cross dimer with a ΔG of -5 kcal/mol and an internal cross dimer with a ΔG of -6 kcal/mol is tolerated generally.
2. Repeats: Avoid di-nucleotides such as ATATAT. Maximum number of di-nucleotide repeats acceptable in an oligo is 4 di-nucleotides.
3. Cross homology: Test primers to avoid amplifying other genes in the mixture by blasting at NCBI Blast

Storage:

1. Store in the dark
2. Stable at 4°C in dH20 for up to 60 weeks
3. Can be frozen at -20°C

References

• http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
• http://www.idtdna.com/calc/analyzer