Consider a jigsaw puzzle. While most of the pieces have a different picture on their surface, all pieces fit together in an interlocking pattern.
As unlikely as it may seem, restriction enzymes from different organisms can produce interlocking pieces of DNA – so called compatible cohesive ends (CCE). These are pieces of DNA, which fit together and can be ligated, creating a hybrid molecule.
It’s all about isoschizomers
The recognition sequences of type II restriction enzymes used in molecular biology are palindromic, e.g. symmetrical. Further constraints on the restriction enzymes are the requirements to recognize certain bases in certain positions of a palindrome. The result is a finite number of the solutions for DNA recognition and cleavage puzzle – a lot of different species have unrelated enzymes, which recognize the same sequence (they are called isoschizomers).
Of course, by definition, isoschizomers often produce compatible cohesive ends. However, unrelated enzymes with different recognition sequences can also produce compatible ends, which can be ligated together. Have a look at Figure 1 in which two different DNA molecules, cleaved by Cla I and BstB I, respectively, can be ligated together. In this case the resulting, hybrid molecule can be further re-cleaved by the third enzyme, Taq I. Conversely, ends cleaved by Taq I are compatible with Cla I and BstB I and several other enzymes.
Figure 1. Example showing the generation of compatible cohesive ends.
Putting isoschizomers to work for you
You can see from Figure 1 that using CCE destroys both original recognition sequences.
So what’s the point in using CCE for cloning?
Well, sometimes it’s the only way to ligate, saving the necessity of a PCR.
More importantly, destruction of the restriction sites can be a useful diagnostic tool to distinguish between your vector self-ligation and the resulting construct containing the fragment of interest.
Identifying CCE
How would you know if your enzymes of choice produces CCE?
The simplest, low tech way is looking in the New England Biolabs catalog, which contains a lot of useful information in the last section. In the 2013-2014 edition the list of enzymes producing CCE, what they can be ligated to and how to re-cleave hybrid molecules is located on pages 312 – 314. Alternatively, NEB also provide this information on their website.
Let’s have fun with DNA jigsaw puzzle!
More 'DNA / RNA Manipulation and Analysis' articles
Whether you need to get your plasmid DNA to a lab on the other side of the world, or a few hundred miles down the road, it’s important to make sure your precious sample gets there, it is not degraded, and you don’t end up in jail. Here’s the Bitesize guide on how to send…
While they may not be as in demand as when they were the basis of sequencing projects, bacterial artificial chromosomes (BACs) are still used for a wide variety of projects. Based off of the F origin of replication, BAC vectors can stably maintain up to 300 kb of sequence in a single plasmid, lending themselves…
Whatever molecular biology techniques you use, at some point you will have to clean up your DNA samples to remove things like buffers, contaminants and nucleotides from you precious sample, so that you have perfectly pure DNA for your downstream experiments. Magnetic beads are one DNA cleanup option. They are simple and effective—and their reassuringly…
Collecting biological samples in the field can be difficult, since storage conditions outside of the lab are often less than optimal. Enter the Whatman FTA (Flinders Technology Associates) Cards. The Whatman FTA Card, a filter paper product manufactured by GE Health Care, is a paper matrix laced with a proprietary mixture of chemicals that lyse…
Overnight ligations are inconvenient — especially when they fail. Luckily, there’s a straightforward way to faster DNA ligations. This article highlights the secret ingredient to faster ligation reactions and offers some tips and caveats on its use. For a general overview of DNA ligations, see here and here. Buy a Quick Ligation Kit The most…
10 Things Every Molecular Biologist Should Know
The eBook with top tips from our Researcher community.