Figure 1. Schematic structure of RNA and DNA. Outlined is the chemical composition of the phosphodiester backbone of both RNA and DNA. The hydroxyl group at the 2¢ position of the ribose sugar in RNA is indicated in red. In DNA a hydrogen atom replaces the hydroxyl group. The polarity of the DNA or RNA strands are determined by whether a phosphate or hydroxy terminus is attached to either the 3¢ or 5¢ carbon of the sugar moiety. The N-glycosidic bond through which the purine and pyrimidine bases are attached to the sugar is highlighted in blue. A, adenine; G, guanine; C, cytosine; T, thymine; and U, uracil.

Figure 2. Cleavage of phosphodiester bonds by exonucleases or endonucleases. Endonucleolytic cleavage of either an RNA or DNA substrate takes place at internal sites. They can generate either 3¢-PO₄ and 5¢-OH (indicated in red) termini or 3¢-OH and 5¢-PO₄ termini. Exonucleolytic degradation starts at a terminus. If it proceeds via a hydrolytic mechanism, nucleoside monophosphates are released. When a phosphorolytic mechanism is employed, inorganic phosphate (P_i) is required and nucleoside diphosphates are released. This reaction is reversible.

Figure 3. Special types of nuclease substrates. Apurinic DNA. Apurinic sites are generated when the N-glycosidic bond (see Figure 1) is cleaved. The apurinic site (in red) represents a noncoding region because of the loss of either the purine or pyrimidine base that had previously been attached. DNA containing a UV-induced thymine–thymine dimer (red). The formation of this photoproduct results in the breaking of Watson–Crick base pairs and the formation of a local distortion in the DNA duplex. RNA/DNA hybrid. RNA(blue)/DNA hybrids are generated during the process of DNA replication initiation as well as under circumstances where RNA molecules are converted into DNA. RNAase III substrate. RNAase III recognizes specific stem–loop structures in RNA molecules and can cleave on either one side or both sides of the stem.