9 Nucleases Involved in DNA Repair

Abstract

I. A WORD ON NOMENCLATURE
The problem of nomenclature is especially acute in the case of repair nucleases. The most critical problem arises from the discovery of “AP endonucleases” that act through a β-elimination (lyase), rather than by a hydrolytic mechanism (see Chapter 1). Because these enzymes are generally thought of as “nucleases” by investigators outside the field of repair, and because they clearly fall into the purview of “DNA-repair nucleases,” they are included in the list of “repair nucleases” noted here; i.e., they are proteins that catalytically cleave phosphodiester bonds within a polynucleotide.

A second problem of nomenclature arises when proteins have several names due to their having been independently isolated by several laboratories, possibly assaying separate activities, or when homologous enzymes have been isolated from several organisms. In this chapter, we refer to them by their accepted gene name (e.g., Escherichia coli Fpg protein) or by their E. coli designation where several bacterial homologs have been described (e.g., exonuclease III).

II. TYPES OF DNA DAMAGE AND CAUSATIVE AGENTS
Virtually all DNA-damaging agents cause multiple types of lesions, and most lesions can be formed by several agents. In addition, the major biological response to a DNA-damaging agent might not be elicited by the most abundant lesion produced. For these reasons, it is not always possible to prepare specific substrates for particular nucleases or to identify specific nucleases involved in processing these particular lesions. The following types of DNA damage are intended to exemplify the situation and to illustrate the...