Harpers

DNA ORGANIZATION, REPLICATION, & REPAIR / 337Base Excision-RepairThe depurination of DNA, which happens spontaneouslyowing to the thermal lability of the purine N-glycosidic bond, occurs at a rate of 5000–10,000/cell/dat 37 °C. Specific enzymes recognize a depurinated siteand replace the appropriate purine directly, without interruptionof the phosphodiester backbone.Cytosine, adenine, and guanine bases in DNA spontaneouslyform uracil, hypoxanthine, or xanthine, respectively.Since none of these normally exist in DNA,it is not surprising that specific N-glycosylases can recognizethese abnormal bases and remove the base itselffrom the DNA. This removal marks the site of the defectand allows an apurinic or apyrimidinic endonucleaseto excise the abasic sugar. The proper base isthen replaced by a repair DNA polymerase, and a ligasereturns the DNA to its original state (Figure 36–23).This series of events is called base excision-repair. By asimilar series of steps involving initially the recognitionof the defect, alkylated bases and base analogs can be removedfrom DNA and the DNA returned to its originalinformational content. This mechanism is suitablefor replacement of a single base but is not effective atreplacing regions of damaged DNA.Nucleotide Excision-RepairThis mechanism is used to replace regions of damagedDNA up to 30 bases in length. Common examples ofDNA damage include ultraviolet (UV) light, which inducesthe formation of cyclobutane pyrimidine-pyrimidinedimers, and smoking, which causes formation ofbenzo[a]pyrene-guanine adducts. Ionizing radiation,cancer chemotherapeutic agents, and a variety of chemicalsfound in the environment cause base modification,strand breaks, cross-linkage between bases on oppositestrands or between DNA and protein, and numerousother defects. These are repaired by a process called nucleotideexcision-repair (Figure 36–24). This complexprocess, which involves more gene products than the twoother types of repair, essentially involves the hydrolysis oftwo phosphodiester bonds on the strand containing thedefect. A special excision nuclease (exinuclease), consistingof at least three subunits in E coli and 16 polypeptidesin humans, accomplishes this task. In eukaryoticcells the enzymes cut between the third to fifth phosphodiesterbond 3′ from the lesion, and on the 5′ side the cutis somewhere between the twenty-first and twenty-fifthbonds. Thus, a fragment of DNA 27–29 nucleotideslong is excised. After the strand is removed it is replaced,again by exact base pairing, through the action of yet anotherpolymerase (δ/ε in humans), and the ends arejoined to the existing strands by DNA ligase.Xeroderma pigmentosum (XP) is an autosomal recessivegenetic disease. The clinical syndrome includes3′5′A T C G G C T C A T C C G A TT A G C C G A G T A G G C T A5′3′Heat energyA T C G G C T U A T C C G A TT A G C C G A G T A G G C T AAUT C G G C T*URACIL DNA GLYCOSYLASEA T C C G A TT A G C C G A G T A G G C T AAT C G G CNUCLEASEST C C G A TT A G C C G A G T A G G C T AA T C G G C T C A T C C G A TT A G C C G A G T A G G C T ADNA POLYMERASE + DNA LIGASEFigure 36–23. Base excision-repair of DNA. The enzymeuracil DNA glycosylase removes the uracil createdby spontaneous deamination of cytosine in the DNA. Anendonuclease cuts the backbone near the defect; then,after an endonuclease removes a few bases, the defectis filled in by the action of a repair polymerase and thestrand is rejoined by a ligase. (Courtesy of B Alberts.)marked sensitivity to sunlight (ultraviolet) with subsequentformation of multiple skin cancers and prematuredeath. The risk of developing skin cancer is increased1000- to 2000-fold. The inherited defect seemsto involve the repair of damaged DNA, particularlythymine dimers. Cells cultured from patients with xerodermapigmentosum exhibit low activity for the nucleotideexcision-repair process. Seven complementationgroups have been identified using hybrid cellanalyses, so at least seven gene products (XPA–XPG)are involved. Two of these (XPA and XPC) are involvedin recognition and excision. XPB and XPD arehelicases and, interestingly, are subunits of the transcriptionfactor TFIIH (see Chapter 37).Double-Strand Break RepairThe repair of double-strand breaks is part of the physiologicprocess of immunoglobulin gene rearrangement. It