Restriction Site Search

(link to screenshot 9) GeneDesigner permits you to search for restriction sites that exist within a construct.

• You can also search for places within an open reading frame where restriction sites could be introduced by making silent mutations.

In Sequence View select the “Find” panel (label in screenshot 9)

• Select the “Restriction Sites” tab
• Select a restriction site group from the pull down list
• Select one or more sites from the list
• Click the “Find” button
  • Results are displayed in a hit list, which displays the position of each site found
  • Clicking on the site in the hit list highlights the site within the local sequence window
• Initiate a new search by clicking on the “back/clear” button

• The default settings are to search for the selected restriction sites within every construct in the project
• To search for the selected restriction sites in a single construct, or just a part of a construct, select the “Restrict Search” button (label in screenshot 9).
  • Selecting this button will restrict the search to constructs or elements that are highlighted in the Navigation Pane.

• Sites that could be introduced by making silent mutations within an open reading frame can be found by checking the “Find potential sites” box (label in screenshot 9).
  • Finding potential sites is computationally more intensive than finding existing sites, so it may be helpful to restrict the search to just the elements of interest when searching for potential sites.

• If a restriction site that is displayed is inhibited by overlapping dam or dcm methylation, than any overlapping dam or dcm methylation site is also displayed.
  • These sites will only be digestible if the construct has been propagated in a methylation deficient host.