Template:Strand gen

Design Considerations

In order to properly perform its role as a DNA computer complex, the following considerations had to be made for the branch migration domains of the part:

• Three nucleotides only (A, T, or C for the top strands and T, A, or G for the bottom strands) to avoid that the strands fold onto themselves
• 30-70% GC content for proper melting temperatures
• No more than 4 As or Ts in a row or 3 Cs or Gs in a row to avoid synthesis errors
• At least 30% base-pair difference between any 2 sequences to avoid unwanted reactions
• The longest run of matches between any 2 sequences is at most 35% of the domain length to avoid unwanted reactions
• A 2-nucleotide clamp domain should be present on either end of the branch migration domains and at the end of toeholds

Note that all toeholds can and do have the same main sequence, since they will unbind if the following branch migration domains are not complementary.