## 6 Global Genome Repair (GGR)  
### Discrimination of Native DNA from Damaged by UvrA  
Of all the DNA repair pathways, NER is distinguished by its capacity to process widely varying DNA lesions [6; 52], including those processed by mechanisms specific to particular lesions [52]. This feature of NER raises a key unresolved question: how do a series of highly conserved proteins accurately identify and repair a diverse set of DNA lesions. It is axiomatic that the structurally and chemically diverse nature of lesions processed by NER precludes direct recognition of DNA adducts. Rather, NER proteins likely recognize common abnormalities of the DNA double helix induced by the structurally varying lesions. Prior studies have suggested that properties such as reduced stability of the double helix, state of unwinding [81; 82], structural distortions, changes in electrostatic properties [83; 84], alterations in base stacking or local flexibility [85], as well as changes in DNA conformational dynamics [86; 87] could be factors leveraged by UvrA to distinguish damaged from native DNA. Decisively addressing this question for both bacterial and eukaryotic NER remains a major line of investigation. UvrA uses the energy from ATP binding and hydrolysis (below) to detect widely varying damaged DNA among the vast excess of normal DNA in the genome. To perform this important function, UvrA must have the capacity to discriminate native DNA from a series of chemically and structurally distinct lesions, including diverse adducts, mismatches, nicks and gaps [52; 88; 89]. UvrA exhibits a 2-5 fold preference for damaged DNA in comparison to undamaged DNA [42; 90]. While precise values for specificity of NER in vivo are difficult to establish owing to multiple confounding factors [91; 92], it is clear that small differences in binding affinity alone cannot account for the exquisite specificity of NER, which is assumed to repair the bacterial genome within the cell division cycle [7]. It has been suggested that kinetic proofreading may play a key role in supplementing differences in binding affinity to explain precision of NER [30; 93; 94; 95; 96]. Kinetic proofreading is a mechanism that allows biological reactions to achieve higher specificity beyond that afforded by differences in free energies of binding between correct and incorrect substrates [97]. The enhanced specificity is made possible by unidirectional energy-utilizing intermediate steps, which generate delays between initial target binding and catalysis; the correct substrate complex survives these delays and moves to the next step, while incorrect substrates do not and dissociate. During NER, the UvrA and UvrB proteins use the energy of ATP binding and hydrolysis to implement a precise sequence of events that begins with damage detection by UvrA and ends with UvrB at the lesion, poised to recruit the UvrC nuclease. The molecular dance performed by UvrA and UvrB on DNA has been considerably illuminated by insightful biochemical, structural and single-molecules studies. The physiological DNA damage sensor in GGR is a complex between UvrA and UvrB whose in vitro stoichiometry has been variously estimated as UvrA\({}_{2}\)B\({}_{2}\) or UvrA\({}_{2}\)B\({}_{1}\)[21; 98; 99; 100; 101]. The UvrA\({}_{2}\)B\({}_{2}\) complex uses three different search modes to locate damaged DNA: (1) free diffusion, in which the complex randomly changes position on DNA; (2) directed motion, where the complex migrates with directionality on DNA; and 3) paused motion, which is characterized by long pauses followed by short bursts of movement [94; 98]. On the other hand, a recent in vivo single-molecule analysis suggested that UvrA alone performs the search for a lesion and that UvrB is subsequently recruited to the damage site by UvrA [38]. With either model, UvrA plays the key role in damage recognition as it is the first protein that establishes contact with the DNA before handing it off to UvrB [18].