While the genetic information encoded in DNA and RNA molecules is directly related to the order of the purine and pyrimidine bases, it is the sugar–phosphate backbone that provides the glue that keeps these molecules intact. It is the function of nucleases to break the stable phosphodiester bonds between the sugar moieties when necessary. Nucleases participate in almost all biological reactions involving either RNA or DNA.

Keywords: DNA metabolism; RNA metabolism; phosphodiester bond cleavage; ribozymes

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 (Pi) 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.


Further Reading

Adams RLP, Knowler JT and Leader DP (1986) The Biochemistry of Nucleic Acids, 10th edn. London: Chapman and Hall.

Deutscher MP and Li Z (2000) Exoribonucleases and their multiple roles in RNA metabolism. Progress in Nucleic Acid Research 66: 67–105.

Linn SM, Lloyd RS and Roberts RJ (1993) Nucleases, 2nd edn. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.

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Kushner, Sidney R(May 2002) Nucleases. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0001034]