Transcription-Coupled Repair and Complex Biology

All active living organisms mitigate DNA damage via DNA repair, and the so-called nucleotide excision repair pathway represents a functionally major part of the cell's DNA repair repertoire [1]. In this pathway, the damaged strand of DNA is incised and removed before being resynthesized. This form of DNA repair requires a multitude of proteins working in a complex choreography. Repair thus typically involves detection of a DNA lesion, validation of that detection event, search for an appropriate incision site and subsequent DNA incision, DNA unwinding/removal, and DNA resynthesis and religation. These activities are ultimately the result of molecules randomly diffusing and bumping into each other and acting in succession. It is also true, however, that repair components are often assembled into functional complexes which may be more efficient or regular in their mode of action. Studying DNA repair complexes for their mechanisms of assembly, action, and disassembly can help address fundamental questions such as whether DNA repair pathways are branched or linear; whether, for instance, they tolerate fluctuations in numbers of components; and more broadly how search processes between macromolecules take place or can be enhanced.