sophisticated restriction site analysis

Gene Construction Kit provides users with lists containing all known restriction enzymes with which to work, while also providing lists containing only commercial enzymes or enzymes sorted by recognition sequence lengths. Users can choose to mark enzyme sites by how many times they cut a sequence, by the kind of cut they create (5', 3', blunt), or even by whether or not they cut within a specified segment. One can even generate a table output of 'No cutters' for a specific selection of DNA. This flexibility allows sophisticated searching - such as marking all unique blunt end cutters that cut only within a selected segment of DNA; or - marking all enzymes that cut more than 5 times, but only cut outside a selected segment.

Restriction Analysis

customizable enzyme lists

GCK also allows users to add or modify enzyme list entries - change the recognition site, update the cut site, or even choose a new name to display for an enzyme entry. Additionally, users can create and save their own unique list file containing, for example, only enzymes that are routinely used in the lab. These 'custom' enzyme list files are available for use when marking or listing sites within GCK.

Restriction Analysis

In addition to storing restriction enzymes, GCK list files can also be used to store, and subsequently identify, small stretches of DNA sequence a user might be interested in quickly marking in new DNA constructs. Sequences representing linkers, promoters, primers, poly(A) signals or TATA boxes can be stored in list files - and are then available to be used in the Mark Sites and List Sites analyses. This type of flexibility is unmatched in the marketplace.

silent mutations

Silent mutations are point mutations in a DNA sequence that do not alter the coding information in that DNA sequence. In cloning projects, there is often a need to manipulate fragments that do not have restriction sites at convenient locations - and sometimes the site of the sequence change may lie within a coding region. GCK allows users to create new (and remove existing) restriction sites by silent mutation through a simple menu selection.

Restriction Analysis