GENtle/Restriction Assistant

GENtle splash screen.png GENtle: Tools and Dialogs

Ligation - Options - Databases - Import - Enter sequence - Sequence editor - Restriction Assistant - PCR troubleshoot dialog - Proteolysis assistant - Projects - Edit primer dialog - Find dialog - Printing - Enzyme management - Sequencing Primers - Silent Mutagenesis - Automatic annotation

The Restriction Assistant can be invoked via menu Tools/Enzyme Assistant, or through a click with the middle mouse button on a restriction site in the DNA map. For the latter, the selected enzyme is automatically selected in the list of "Available enzymes" (left). This list depends on the selections "Group" and "Subselection". It can be sorted by enzyme name or number of cuts by clicking on the respective column title. For a selected enzyme, the resulting fragments are shown in the lower left list.

The Restriction Assistant.

The list on the right shows the contents of the "restriction cocktail", the enzymes already selected for cutting. The resulting fragments for these enzymes together are shown in the lower right list. The enzyme selected in the left list can be put in the cocktail via Add to cocktail; all enzymes from the left list can be added at once via Add all. An enzyme can be removed from the cocktail by selecting it in the right list, then via Remove enzyme.

Do not create fragments below ___ base pairs, when selected, limits the fragments generated to a minimum size. Done exits the restriction assistant while preserving the changes mage to the cocktail, whereas Cancel will void all changes made.

Start restriction (the scissors symbol) will initiate the simulated restriction. The result of this can be influenced by several further settings:

  • Create fragments will generate the actual DNA sequences with their blunt/sticky ends that will result from a digestion with the cocktail. This option is pre-selected.
  • Add to gel will add the fragments to a virtual gel, together in one lane.
  • One lane each will alter the above so that each enzyme gets its own lane.
  • Partial restriction will add all possible fragments to a virtual gel lane, simulating a partial (incomplete) restriction. The option One lane each is not available when Partial restriction is checked.

The restriction cocktail will be preserved so you can cut another DNA with that very enzyme combination, which is useful for an upcoming Ligation.