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.

Please note that depending on the security settings in your browser you may not be able to see the button below to start the program. You may also see a red box or get an error message. To get the program started you need to select "trust this site" if a message pops up or click "Allow" to let run "Java Applet". You may also need to add this site to the trusted sites settings in your browser preferences (security then manage website settings for Java) and/or Java preference panel or control panel (security setting, edit site list). It does work with the right settings!