Oligos

DNADynamos 'Oligo Editor' can help you design oligonucleotide primers against a specific section of DNA sequence. From a DNADynamo window containing the template sequence, select the oligos target sequence, then press the 'Oligo' button to open the oligo editor.

DNADynamo also has an interface to Primer3 primer pair design software. In a DNADynamo window containing the template DNA sequence, press the 'Primer Pair' button to open the Primer3 interface, adjust the parameters as necessary, and press the 'Add' button for pairs that you want to save.

DNADynamo saves oligos that are created with the Oligo Editor and Primer3 interface in the 'Master Oligo Box'. You can open the 'Master Oligo Box' using the menu option 'Boxes' -> 'Master Oligo Box', from where you can review, copy, export, edit or delete your saved oligos. You can also import oligos from txt files in fasta or csv format or from nti oligo archive or database files.

When you display a features map for a sequence, DNADynamo will map oligos that are in the 'Master Oligo Box' and hit the template sequence. You can click oligos displayed on a 'features' map to open a menu of options, which includes displaying the oligo on the template sequence, or editing the oligo in the oligo editor.

By default 'Master Oligo Box' oligos are saved in a file named AllOligosBox.CBY that can be found in your DNADynamo installation folder. The 'Master Oligo Box' menu option 'Manage-Store' options can however be used direct the 'Master Oligo Box' to use a store file in another location eg a shared cloud folder such as DropBox or SkyDrive

A separate 'Vector Sequencing Oligos' Box is available to store common oligos that hit vector sequences, if you would prefer to keep these separate.

You can generate a new DNADynamo window containing the theoretical product of a PCR reaction using two oligos to aid in 'Virtual Subcloning'.