RNA Polymerases A Brief Overview

The behavior of an RNA polymerase at DNA damage can be best understood in light of structural information about the specific RNA polymerase being studied. As Table 17.1 illustrates, studies using site-spedfically damaged DNA have employed bacteriophage, prokaryotic, and eukaryotic RNA polymerases. 

In contrast to the single-subunit RNA polymerase found in bacteriophages, the model prokaryotic RNA polymerase from E. coli is a multisubunit enzyme. This polymerase has a five-subunit core that forms a constricted, tunnel-shaped catalytic site [97]. Prokaryotic RNA polymerases require an additional subunit, a, for promoter-specific initiation of transcription [98, 99]. 

Eukaryotes have three RNA polymerases rather than one, named RNA Pols I, II, and III. Each is responsible for the synthesis of specific RNA molecules RNA Pol I transcribes genes encoding rRNA, RNA Pol II transcribes genes that encode proteins and some other genes that encode regulatory RNA molecules, and RNA Pol III transcribes genes that encode rRNA, tRNA, and other small RNAs. 

Abasic Sites, Single-Strand Nicks, and Caps 

DNA single-strand breaks often result from oxidative damage or during DNA repair. They can be simple nicks in the backbone with no associated loss of a base, or they can occur at sites where the nitrogenous base is absent hence, this class of DNA lesions can differ with respect to the chemistry of the 3 - and 5 -termini at the break site, depending on how they are generated. The structural details of single-strand DNA breaks play important roles in how specific RNA polymerases behave at such sites. 

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