Designing primers

This needs more owrk, 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