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Technicalities of cloning

21 Sep

We live in a time when cloning a gene is a trivial matter done by technicians in the lab using tools that have been around for decades. However, this does not mean that it can be accomplished without knowing precisely how the biology works.

It is often said, even in molecular biology texts, that the DNA of the target gene and a plasmid vector simply need to be cut with the same restriction enzyme so that their ‘sticky ends’ can come together and be ligated into a new construct. This is often diagrammed as a cut and paste procedure (below), suggesting that no further attention to detail is required.

There are two issues (the bulleted items) I have with such a simplified cartoon:

  • This cartoon does not indicate any preference for the direction that the insert takes once it is incorporated into the plasmid.

Inserts have directionality. A gene has a start codon on one end and a stop codon on the other. These must be in line with the promoter sequence and polyA signals that are typically not a part of the insert, but are contributed by the plasmid.

The Promoter sequence is required for binding of the DNA-Dependent RNA-Polymerase that will make the mRNA. This must be upstream of the start codon, ATG. The Poly Signal is responsible for attaching untemplated ‘A’ residues to the 3′ end of the mRNA. It must be downstream of the stop codon, [TAA/TAG/TGA].

The easiest way to prevent this problem is to ensure directional cloning by cutting each end of the vector and insert with different enzymes that don’t possess compatible ends.

The second easiest way to control for cloning your insert in the wrong way is to have a digest with another enzyme to screen for the proper orientation after miniprepping multiple clones. In the figure below, we can see that there is one XhoI site within the insert and one within the plasmid. Because the one in the insert is offset to one side, the size of the fragments generated by this digestion will depend on the orientation of the insert. Knowing which fragment size is associated with proper orientation of the insert will help us to quickly screen our minipreps by XhoI digestion.

  • This cartoon suggests that the recombinant plasmid is the only product of this ligation reaction.

The other problem with this cartoon is that it assumes that the desired ligation of one insert with one plasmid is the most abundant product, when in fact, it probably occurs in a tiny minority of cases. More likely, the plasmid curls up on itself and religates without the insert being incorporated.

The reason that the plasmid religates is because the two ends of the plasmid can religate and they’re close enough together that they probably run into one another more often than an insert does. The way to prevent this is to recall the chemistry involved in this ligation reaction.

This reaction requires a 3′ hydroxyl group and a 5′ phosphate group to come together to form the phosphodiester bond. This happens on each strand of the DNA and is mediated by a ligase enzyme.

However, only one strand being ligated is sufficient to hold the recombinant plasmid together until it can be fixed inside the cell by DNA repair mechanisms. If you remove the phosphate from the plasmid molecule, it cannot come together and be ligated to itself. Instead, only when an insert is incorporated are there the phosphates required to ligate one strand at either end.

The phosphates can be removed from the plasmid DNA using the enzyme, Calf Intestinal Phosphatase (CIP). The only thing you need to remember is that the CIP must be destroyed at the end of its reaction with the plasmid. Otherwise, it can go on to also dephosphorylate the insert DNA when that is added for a ligation reaction. Luckily, CIP is easily inactivated by heat (NEB suggests 80 C for 2 minutes).

An alternative to CIP is Shrimp Alkaline Phosphatase (SIP), also available from NEB.

Using either of these two techniques individually will result in an abundance of your preferred recombinant product.

Happy cloning!

 
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Posted by on September 21, 2020 in Uncategorized

 

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