Tag: restriction digests

  • Controlling the realism of Agarose Gels

    —

    by

    Chris
    in

    The default settings for the agarose gel display in MacVector generate a reasonable photorealistic simulation of an agarose gel. We have actually boosted the intensity of small bands quite significantly, and reduced their diffusion so that smaller bands show up a little more obviously and crisply than they might in real life. Even so, you…

  • A few tips on working with digested fragments in the Cloning Clipboard

    —

    by

    Chris
    in ,

    The Cloning Clipboard is an easy, and flexible, way to design and document your cloning strategies. Here’s two tips on manipulating a single fragment. If you drag a fragment from the Cloning Clipboard to a vector, then you’ll get the ligate dialog. However, if you have already selected a pair of enzyme sites, then the…

  • Create constructs using the Cloning Clipboard

    —

    by

    Chris
    in ,

    You can create new constructs in MacVector by selecting two restriction enzyme sites, choosing Edit -> Copy, selecting a target restriction site in a different molecule and then choosing Edit -> Paste. It works great and fully understands compatible overhanging sticky ends preventing you from accidentally creating biologically impossible molecules. However, a far more flexible…

  • Removing a restriction site from a plasmid with the Cloning Clipboard

    —

    by

    Chris
    in

    Being able to remove a restriction site by digesting with an enzyme that cuts at one site to linearize a plasmid, Klenow treating the linear fragment, then religating the fragment, is a useful trick in the lab. It can help you produce a suitable, and simple, cloning site when none previously existed in your vector.…

  • Keep up to date with MacVector auxiliary files

    —

    by

    Chris
    in

    MacVector has a large collection of data files that are installed in folders alongside the MacVector application. These include Restriction Enzymes files, Scoring Matrices, documentation, tutorials, a variety of common cloning vectors and even a few useful Applescripts. If you use MacVector’s built-in automatic updater to install each new release and bug-fix, you will find…

  • How to select all identical restriction enzyme sites

    —

    by

    Chris
    in

    The Automatic Restriction Enzyme Analysis tool that is displayed on the sequence in the Map tab is very powerful. It automatically displays a custom set of restriction enzyme recognition sites on every sequence that you open. Unique recognition sites are displayed in red and sites with two or more cut locations are displayed in blue.…

  • Restriction enzyme sites in cloning vectors show compatible ends with fragments in the Cloning Clipboard

    —

    by

    Chris
    in

    If you are looking for compatible cloning sites for a fragment, MacVector has a simple color-coded function to identify potential target sites in a vector. First select the fragment you wish to clone by clicking on two enzymes in the Map view of a single sequence document or from a restriction enzyme search result. Then…

  • Restriction enzyme sites and tooltips

    —

    by

    Chris
    in

    Quickly viewing the recognition sequence and cut site of a restriction site is very easy in the Map tab. If you hover your mouse over a restriction site in the Map tab, a tooltip will show you the restriction enzyme recognition site, the location of the cut site, and number of times that enzyme cuts…

  • Use the [option] key to paste, or ligate, in the opposite orientation

    —

    by

    Chris
    in

    The most simple way of generating new constructs in MacVector using restriction enzyme sites is to: [shift]-select two sites in the Map tab of a source molecule. Switch to the Map tab of a target vector. Select the corresponding site(s) there. Simply choose Edit | Paste to insert the copied fragment into the target molecule.…

  • Simulated Agarose Gels

    —

    by

    Chris
    in , ,

    MacVector 14.5 has a Agarose Gel interface which allows you to view photo-realistic recreations of restriction digests of linear and circular DNA molecules. The gels look so realistic that users have had a hard time telling photos of their own digests from the simulation in MacVector. When you first use the new tool and compare…