Dinucleotide

A dinucleotide is a molecule consisting of two nucleotides linked by a phosphodiester bond. In the backbone of nucleic acids, this linkage typically joins the 3' hydroxyl group of one sugar to the 5' phosphate of the adjacent nucleotide, resulting in a molecule with a 5'-phosphate terminus on one end and a 3'-hydroxyl terminus on the other. Dinucleotides can occur as discrete short fragments during nucleic acid metabolism or as transient intermediates in synthesis and repair processes.

The two nucleotides in a dinucleotide can be any combination of the standard bases (adenine, cytosine, guanine, thymine or uracil, depending on DNA or RNA context). The bond is a single phosphodiester linkage, and the dinucleotide generally bears a single 5' phosphate at one terminus and a free 3' hydroxyl at the other. Variants may differ in the phosphorylation state at the ends, but the core feature is the two-nucleotide sequence connected by one phosphodiester bond.

In addition to simple dinucleotides, biological systems include dinucleotide polyphosphates, where two nucleosides are connected by chains of two or more phosphate groups (for example Ap3A, Ap4A). These molecules can function as signaling and regulatory entities in bacteria and eukaryotes, influencing processes such as energy sensing, stress responses, and translation.

Analytical and laboratory contexts view dinucleotides as model substrates for nucleic acid enzymes and as short oligonucleotides in binding or assay studies. They can be synthesized or isolated for biochemical research, with detection and quantification commonly performed by methods such as chromatography or mass spectrometry.