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 3 carbon of the adjacent nucleoside. Specifically, it is the phosphodiester bonds that link 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 involved saccharide groups are deoxyribose in DNA and ribose in RNA. In order for the phosphodiester bond to form, joining the nucleosides, 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.