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Primo SiteD 3.4: Site-directed Mutagenesis Oligo Design           Click here for more PCR primer design tools.
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Primo SiteD 3.4 --- Site Directed Mutagenesis Primer Design

How to use Primo SiteD 3.4 --- Site Directed Mutagenesis Primer Design (beta-testing)

  • Input your DNA sequences by copy and paste. Numbers and blank spaces will be ignored. Degenerate nucleotide codes can be accepted.

    Mutations are shown in parenthesis in the following format:

    ( original sequences, mutated sequences)

    For example (CC, TG) means the sequences "CC" will be mutated to "TG", (CC, ) means "CC" will be deleted, and (,TG) means "TG" will be inserted.

  • Click on the "Go" button to start.
  • For multiple sequences, please input your sequences in the following format:
    
    >Name of Sequence 1
    
    1 ggccgggcgc ggtggctcac gcctgtaat(c,g) ccagcacttt gggaggccga ggcgggtgga
    61 tcacctgagg tcaggagttc gagaccagcc tggccaacat ggtgaaaccc cgtctctact
    121 aaaaatacaa aaattagccg ggcgtggtgg cgggcgcctg taatcccagc tactcgggag
    181 gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtgagc cgagatcgcg
    241 ccactgcact ccagcctggg caacaagagc gaaactccgt ctcaaaaaaa a
    
    >Name of Sequence 2
    aaaaatacaa aaattagccg ggcgtggtgg cgggcgcct(g, ) taatcccagc tactcgggag
    gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtgagc cgagatcgcg
    ccactgcact ccagcctggg caacaagagc gaaactccgt ctcaaaaaaa a
    
    >Name of Sequence 3
    61 tcacctgagg tcaggagttc gagaccagcc tggccaacat ggtgaaaccc cgtctctact
    121 aaaaatacaa aaattagccg ggcgtggtgg cgggcg(,at)cctg taatcccagc tactcgggag
    181 gctgaggcag gagaatcgct tgaacccggg aggcggaggt tgcagtg
    
    
  • For melting temperature calculation, the nearest neighbor formula is used.
  • Choose either "Forward" or "Reverse" primer if the PCR protocol is used. If template is single-stranded DNA, the primer that is complementary to the single-stranded DNA must be chosen.

    For more PCR primer design tools, please visit Primo Home.

    Protocols

    Site-directed Mutagenesis using PCR
    Stratagen Quick-Change

    Others

    Nobel Prize
    PCR Glossary

    Thanks for using Primo SiteD 3.4! Please let us know your suggestions and comments.

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