Assembly PCR Oligo Maker:
A Tool For Designing Oligodeoxynucleotides For Constructing Long
DNA Molecules
Assembly PCR Oligo Maker is created to automate the
design of oligodeoxynucleotides for the PCR based construction of
long DNA molecules. This application is designed specifically to
aid in the design of DNA molecules that are to be used for the production
of RNA molecules by in vitro synthesis with T7 RNA polymerase.
The input for Assembly PCR Oligo Maker is either the
desired DNA sequence to be made, or an RNA sequence. If RNA is the
input the program first determines the DNA sequence necessary to
produce the desired RNA molecule. The program then determines the
sequences of all the oligodeoxynucleotides necessary for a two-step
assembly PCR-based synthesis of the desired DNA molecule.
The output oligodeoxynucleoide sequences are designed
to have a uniform melt temperature and are checked for regions of
overlap outside of the desired priming regions necessary for the
PCR.
