MadSci Network: Molecular Biology |
That is an excellent question! Ligases form phosphodiester bonds between neighboring nucleotides in DNA. This reaction is more efficient if the two ends to be ligated are complementary (“sticky”), but some enzymes will also join blunt ends (without one of the strands being longer by a few nucleotides than the other). Ligases can, of course, also join the ends of a nick in DNA (one phosphodiester bond broken somewhere within a double stranded piece of DNA). At any rate, one of the two nucleotides to be joined needs to have a hydroxyl on carbon 3 of its deoxyribose sugar. The other ligation partner needs to provide a phosphate group linked to carbon 5 of its deoxyribose sugar. Formation of a phosphodiester bond requires the input of energy, so the ligation reaction is coupled with an exergonic (energy releasing) reaction, such as the hydrolysis of a phosphoanhydride bond. Some ligases use the general “energy currency” adenosine triphosphate (ATP) for that purpose, others another nucleotide (NAD+ = nicotinamide adenine dinucleotide). Such molecules are generally referred to as coenzymes, indicating that they are essential participants in the chemical reaction (ligation in this case) that is catalyzed by the enzyme. That is the short version of the answer. If you have a good background in chemistry, you will understand the following summary of the chemical reaction sequence going on as the enzyme links the two nucleotides. The adenosine monophosphate portion of the ATP or NAD+ is first covalently linked to the enzyme itself, then transferred to the phosphate end of the two nucleotides to be joined, to create a phosphoanhydride bond. This bond is then attacked by the hydroxyl group on the other of the two nucleotides to be linked and is replaced by a phosphodiester bond between the hydroxyl and the phosphate of the neighboring nucleotides, thereby ligating the two. Adenosine monophosphate leaves the enzyme, which can now catalyze another round of ligating two nucleotides.
Try the links in the MadSci Library for more information on Molecular Biology.