User:Diatomcymbella/sandbox

In chemistry, a phosphodiester bond occurs when exactly two of the hydroxyl groups (\sOH) in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. The "bond" involves this linkage C\sO\sPO2-O\sC. Discussion of phosphodiesters is dominated by their prevalence in DNA and RNA, but phosphodiesters occur in other biomolecules, e.g. acyl carrier proteins, and the cyclic forms of GMP and AMP (cGMP and cAMP) .

Phosphodiester bonds make up the backbones of DNA and RNA. In the phosphodiester bonds of nucleic acids, a phosphate is attached to the 5' carbon of one nucleoside and to the. The 3' carbon of one the adjacent nucleoside is bonded to the 5' phosphate of the adjacent sugar. Specifically, it is the phosphodiester bonds that link s the 3' carbon atom of one sugar molecule and the 5' carbon atom of another (hence the name 3', 5' phosphodiester linkage used with reference to this kind of bond in DNA and RNA chains). The se involved saccharide groups are derived from deoxyribose in DNA and ribose in RNA. In order for the phosphodiester bond to be form, ed and joining the nucleosides to be joined, the tri-phosphate or di-phosphate forms of the nucleotide building blocks are broken apart to give off energy required to drive the enzyme-catalyzed reaction. In DNA replication, for example, formation of the phosphodiester bonds is catalyzed by a DNA polymerase enzyme, using a pair of magnesium cations and other supporting structures. Formation of the bond occurs not only in DNA and RNA replication, but also in the repair and recombination of nucleic acids, and may require the involvement of various polymerases, primers, and/or ligases. During the replication of DNA, for example, the DNA polymerase I leaves behind a hole between the phosphates in the newly formed backbone. DNA ligase is able to form a phosphodiester bond between the nucleotides on each side of the gap.

Phosphodiesters are negatively charged at pH 7. The negative charge attracts histones, metal cations such as magnesium, and polyamines [needs citation]. Repulsion between these negative charges influences the conformation of the polynucleic acids.

Breaking the Phosphodiester Bond
Hydrolysis (breaking) of phosphodiester bonds is catalyzed by phosphodiesterases. These enzymes are involved in repairing DNA and RNA sequences [5], nucleotide salvage, and in the conversion of cGMP and cAMP to GMP and AMP, respectively. The phosphodiester linkage between two ribonucleotides can also be broken by alkaline hydrolysis, whereas the linkage between two deoxyribonucleotides is more stable under these conditions. The relative ease of RNA hydrolysis is an effect of the presence of the 2' hydroxyl group.