It takes a real effort to keep your basic knowledge of molecular and cell biology fresh, in addition to everything else you have to do. Wouldn’t it be great to if there was a place where you could find easy-to-read articles that allow you to brush-up on those basics in just a couple of minutes?
…I hope you said “yes”, because this is the aim of my “The Basics:” series of articles, which I will be bringing to you periodically (Feel free to let me know whether you think this is a good or bad idea either in a comment or by hitting the “contact” button above). This article explains the basics of DNA ligation. I hope you find it useful.
DNA ligase (EC 188.8.131.52) covalently joins the phosphate backbone of DNA with blunt or compatible cohesive ends (see figure on top right) and it’s natural role is in repairing double strand breaks in DNA molecules. In molecular biology it is commonly used for the insertion of restriction enzyme-generated DNA fragments into vector backbones. Commercial ligases are supplied with a reaction buffer containing ATP and Mg2+, which are both essential for ligase activity. Since ATP can be damaged by repeated freeze-thaw cycles, it is advisable to make aliquots of the buffer (see my article “5 DNA ligation tips“).
The ligation reaction itself has two basic steps. Firstly the DNA ends have to collide by chance and stay together long enough for the ligase to join them. This is the most inefficient part of the reaction, but is easier at low temperatures. Why? Well, as you will probably know, all molecules move faster at higher temperatures so you can imagine that it is going to be easier for two DNA ends to collide and stay together if they are gently floating through the solution at low temperature, rather than whizzing about as they would be at higher temperatures. For cohesive ends, there is an additional reason; lower temperatures stabilize the hydrogen bonding between the complementary nucleotides, which really helps to keep things in place.
The second step is the enzymatic reaction, which is shown schematically in the figure on the left. DNA ligase catalyzes the joining of the 3′-OH to the 5′-phosphate via a two step mechanism. First, the AMP nucleotide, which is attached to a lysine residue in the enzyme’s active site, is transfered to the 5′-phosphate. Then the AMP-phosphate bond is attacked by the 3′-OH, forming the covalent bond and releasing AMP. To allow the enzyme to carry out further reactions the AMP in the enzyme’s active site must be replenished by ATP.
The DNA ligase enzyme has optimal activity at 25°C so the ligation reaction is carried out at a temperature that is a trade-off between the optimal temperatures for bringing the DNA ends together (1°C) and the enzymatic reaction (25°C). Normally 1hr at 16°C is fine but since bringing the DNA ends together is the least efficient part of the reaction favoring this by lowering the temperature to 4°C can give even more efficiency. However, the enzyme will work very slowly at this temperature so a long (e.g. overnight) incubation time is required.