4/28/2016
Importing the FastDigest Restriction Enzyme Collection into Vector NTI
Advance
Open the Vector NTI Explorer (the Database Module).
To import the FastDigest Enzyme Archive (FastDigest.ea4 ), go to Table Menu and
Choose Enzymes.
Go to the Table Menu again and choose Import Molecules from Archive. If you do not
see the Table Menu, choose the Enzyme menu and follow the same instructions.
Navigate to the Location where the Archive file .ea4 has been saved, click on the file
you want to import and select open.
You will be given the option to save the enzymes into a Subset. The name of the archive
file will be suggested as the name of the subset. You can choose not to save into a
subset by clicking on Enzymes (MAIN) in the pop-up window. Subsets are
recommended in this case as they can help you to easily access the FastDigest
enzymes when you are performing cloning activities in Vector NTI.
If you see a pop-up window like the following, click yes.
If there are enzymes with the same name already in your database (this should not be
the case) please choose Overwrite All, and then press OK.
The files have now been imported and if you chose to create a subset, it has now been
created and populated with the enzymes you have just imported
Creating a Subset with Just the FastDigest Enzymes
If you chose not to make a Subset when importing the Enzymes, but would like organize
the enzymes into a subset at a later date, please do the following.
Right click in the Enzymes Text Pane on the left hand side of the screen, and choose
Subset. Name the subset by typing a name in the Subset title box. Scroll down to the
FastDigest section of the Enzymes Database. Click on the first FastDigest enzyme in
the list and then hold the control and shift keys and click on the last FastDigest enzyme
in the list. This will select all of the FastDigest enzymes in the database. Drag this
selection into the newly created Subset.
Finding Unique Cutters in a Multiple Cloning Site of a Vector
Choose vector in the Exploring – Local Vector NTI Database
Note the region of the vector sequence which corresponds to the Multiple Cloning Site
(in this example the MSC is 895 bp to 1010 bp).
In the Vector NTI window, click on the Analysis menu and choose Restriction Analysis
and then Restriction Sites. The Restriction Analysis window will appear.
Click on >> Remove All to clear the current list if necessary. Then Click <Add
You can select all of the enzymes in a given subset by choosing the Subset from the
“Look in” Drop Down menu.
Once the enzymes in that subset are populating the window, click Select All and then
OK.
Alternatively, if only a few of the enzymes are desired click on the first enzyme to be
added and then hold the Shift key as you click on the next enzyme that is required. If
several enzymes which are listed consecutively in the list are desired, hold down the
control and shift keys while you click on the first and the last enzymes in the list. Please
note this can be done several times, each time adding more enzymes to the list.
Once you have selected the enzymes you would like to examine, click ok.
Also if isoschizomers are of interest, the list can be ordered by the recognition site; this
can be achieved by clicking on the Recognition String column header (the result is
pictured below).
Once the list of potential Restriction Enzymes has been established, establish the
frequency of cuts you would like to see by defining Ignore RENs having “less than” or
“more than” sites and also establish the Multiple Cloning Site by defining the “Ignore
REN’s cutting outside region”.
Once you have set the search criteria, click OK to run the Restriction analysis.
The Restriction Enzymes which meet these criteria will be noted with a yellow file folder
and a Plus sign (+) in the text pane. They will also be displayed on the vector map in
the graphics pane, and written above the sequence in the sequence pane.