Designing primers: Difference between revisions
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This needs more | This needs more work, but wanted to get it started. | ||
Some general rules: | Some general rules: | ||
Revision as of 11:10, 23 May 2005
This needs more work, but wanted to get it started.
Some general rules:
- Avoid runs over 3 nucleotide (AAAA)
- 18-30bp in length (what about tails?)
- 3’ end should be G or C (stronger bond)
- primer melting temp (Tm) should be 50-60C w/ low FIR difference (<5C, 2C better)
- 30-80% GC (>50% is better)
- avoid palindromes
- check for dimer binding and hairpins in Vector NTI
- want to avoid structures with ΔG < -5kcal/mol
