Creating Oligos and Using The Oligo Editor

To create a new oligo, in a DNADynamo DNA sequence window, select the target DNA sequence with the mouse and press the 'Oligo' button, or open the 'Master Oligo Box' and press the 'New' button


The oligo editor is opened

You can edit the oligos sequence as you might expect ie by placing the cursor and using your keyboard.

So for example, you could type in a BamHI sequence 'GGATCC' at the 5' end of the oligo if needed

You can also use 'translated' mode - by pressing the 'Mode' button - and select an amino acid, type a replacement, and select the codon to use

If you are designing a 'reverse' / 'anti-sense' oligo, you can press the 'anti-sense' button. When this button is pressed, the oligos 'required sequence' is the reverse-complement.




You can enter a name for the oligo, and optionally a creator

If you want to copy the oligos sequence and paste it into another program (eg an order sheet) press the 'copy to clipboard' button

Finally, press the 'Add oligo to box' button to save the oligo in the 'master oligo box'.

Oligo's saved in the master oligo box appear on sequences features maps.


Inserting Restriction Sites and other Short Fragments of DNA from a pre-saved list

Pressing the 'Insert' button opens a list of short DNA fragments including common restriction sites used in subcloning. To insert a fragment at the current cursor position, either double click it with the mouse or select with the mouse and press 'Insert'. To add your own custom fragment to the list, type in a new name and sequence in the labelled text boxes and press the 'Add New Sequence' button.

About The Oligos Target Sequence

You can set a specific 'target' sequence for each oligo. 'Features' maps have two modes for displaying potential oligo hits within their sequence. The two modes are referred to as 'Targets' and 'Locations'. The oligos target sequence is used in 'Targets' mode. If an oligos 'target' sequence is present in the sequence the features map is drawn for, the oligo will appear on the 'features' map. Note that the target sequence can be different from the oligos actual sequence. 'Targets' are therefore a way of guaranteeing that an oligo will be mapped on any given template DNA containing the target sequence. 'Located' mode does not use the set oligo 'target' to map oligos, but instead relies upon 14bp of sequence at the 5' or 3' end of the oligo, being present in the template DNA

For example, a forward PCR oligo might have a target sequence of
ATGGATCGTAGACGAC
but an actual sequence of
GGATCCATGGATCGTAGACGAC
as a required BamH1 site shown in red at the beginning of the oligo is not present in the target gene itself.

Thus the 'target' is the sequence you intend the oligo to initially anneal to, while the actual sequence is the full sequence of the oligo you'll order. When you create an oligo by selecting sequence from the main sequence display, the oligos target sequence is automatically set as the sequence you selected. However, if you create an oligo by selecting the 'New' button, the target sequence must be set manually by selecting the target sequence from the OligoEditors editable sequence display and pressing the 'Set Target' button. For sequencing oligos, the target and actual sequence will remain identical, but for PCR and mutagenesis oligos they will probably differ.

Sense and Anti-Sense
Choose between 'Sense' or 'Anti-Sense' by selecting the appropriate button. The OligoEditor has been designed with the belief that when designing oligos against gene sequences it is conceptually easier to think about and edit oligos in the '+ sense'. The oligos editable sequence display and the oligos 'target sequence' display are presented as the '+strand' view. Selecting the 'anti-sense' option results in the '5'-3' sequence of required oligo box' to display the 'reverse-complement' of the editable view of the oligo, which is the format generally used when ordering oligos.

for example, in the sequence

AGCATGGAAATCATTGAGGTCTCCTGAGAAGAAAGACACTT
 S  M  E  I  I  E  V  S  Z
if an oligo was required to reverse PCR from the stop codon and add an EcoRI site and the sequence shown in bold was selected as the 'target' sequence the editable sequence display would show

GAAATCATTGAGGTCTCCTGAGAATTC

its target display would show

GAAATCATTGAGGTCTCCTGA

and if the anti-sense button was pressed, the required oligo 5-3' box would display GAATTCTCAGGAGACCTCAATGATTTC

To order an Oligo in the 'Real World' the oligo sequence from the 'Required Oligo 5-3' Sequence' display may be copied to the System Clip-Board and subsequently pasted into your order form. Alternatively, the sequence displayed alongside an oligos name and comments in the 'Oligo Box' display also represents the Required Oligo 5-3' Sequence and may be selected with the mouse and copied to the clipboard.

If you don't like the 'anti-sense' button
If you don't like the way the anti-sense button operates, don't use it. You can create oligos using the 'New' button in the 'Master Oligo Box' by typing or pasting in any sequence you like, or you can use the 'anti-parallel' option in the 'Sequence' menu to convert the editable view to the 'reverse-complement'

Oligo Type
You can select 'Sequencing','PCR', 'Mutagenesis' or 'Other' to indicate the oligos intended purpose. Setting an oligos type allows users to limit oligo box displays to oligos of a certain type.

Editing and Deleting Oligos
Open the 'Master Oligo Box' using menu option 'Boxes' -> 'Master Oligo Box'. Here you can select oligos and either delete ot edit them. Alteratively you can click an oligo displayed on a features map and select 'edit' from the pop up menu

To enter a new Vector Sequencing Oligo, press the 'New' button in the 'Vector Sequencing Oligos Box' and enter the sequence as described above.