DNA Replication and Repair

Section IV describes the structures and functions of the nucleotides and nucleic acids, and covers many major topics such as DNA replication and repair, RNA synthesis and modification, and protein synthesis. It also discusses new findings on how genes are regulated and presents the principles of recombinant DNA technology. 

In some circumstances, DNA radical lesions can react with an adjacent base or the sugar residues. In these cases, a single radical hit can be transformed into two adjacent damage sites on the DNA. The resulting tandem lesions may present special challenges to DNA replication and repair systems. ... 

Ligation The joining of two DNA strands to each other to form a 5 to 3 phos-phodiester linkage. The reaction is catalysed by the enzyme DNA-ligase which is important in DNA replication and repair and when purified it is used for joining DNA in vitro. 

A second relevant enzyme to 5-FU metabolism is thymidylate synthetase (TYMS). If this enzyme is complexed with 5-FU metabolites along with 5,10-methylene-tetrahydrofolate, it cannot maintain a thymidine-5 -monophosphate pool required for DNA replication and repair. A tandem repeat polymorphism in the 5 -promoter region of the TYMS gene can increase enzyme expression (85,86). Tumors carrying the repeats have higher enzyme expression, resulting in lower response to chemotherapy compared to wild type (87). 

Mechanism of Action A fluoroquinolone that inhibits the DNA enzyme gyrase in susceptible microorganisms, interfering with bacterial DNA replication and repair Therapeutic Effect Produces bactericidal activity... 

How complex can the proteome of hydrogenosomes in T. vaginalis be expected to be Trichomonad hydrogenosomes have lost many standard metabolic capacities of mitochondria like—and consequently most of the proteins involved in—the tricarboxylic cycle, membrane-bound electron transport and ATP-production (Muller 1993), or fatty acid synthesis (Beach et al. 1990). Because of the absence of a genome (Clemens and Johnson 2000) the complex machineries of DNA replication and repair, gene transcription and protein synthesis are also absent from these organelles. On the other hand, experimental evidence exists for only a small number of metabolic... 

Each chromosome contains DNA, some of which is genes, but it is tightly packaged into chromatin by proteins specialized for folding. There are also proteins (enzymes) necessary for DNA replication and repair and proteins that bind to DNA, such as histones. These are responsible for the organization of chromosomes into nucleosomes. 

Jonsson, Z.O., Hindges, R. and Hubscher, U. (1998) Regulation of DNA replication and repair proteins through interaction with the front side of proliferating cell nuclear antigen. EMBO J., 17,2412-2425. 

Faults in DNA replication and repair in animal cells can lead to a predisposition to cancer. This helps to emphasize the importance of these processes in biology. However, much of our understanding of how they occur at the molecular level has depended upon studies with the simpler bacteria. 

In addition, benzene metabolites appear to be able to inhibit enzymes involved with DNA replication and repair, specifically the topoisomerase enzymes (Chen and Eastmond 1995). Singh et al. (1994) have studied the prooxidant and antioxidant properties of iron-hydroquinone and iron-1,2,4-ben-... 

Chen and Eastmond (1995) showed that benzene metabolites can adversely affect human topoisomerases, enzymes involved in DNA replication and repair. No effect of any metabolite was seen on human topoisomerase I or for topoisomerase II for hydroquinone, phenol, 2,2 -biphenol, 4,4 -biphenol and catechol at concentrations as high as 500 pM. 1,4-Benzoquinone and 1,2,4-benzenetriol inhibited human topoisomerase II in vitro, at 500 and 250 pM without bioactivation. However, following bioactivation, phenol and 2,2 -biphenol showed inhibitory effects at doses as low as 50 pM, whereas 4,4 -biphenol inhibited topoisomerase II at concentrations of 10 pM. 

Not only does DNA form itself into catenated and knotted structures, it also rotaxanates itself with macrocyclic enzymes. A,-Exonuclease [30, 37] is an enzyme that participates in DNA replication and repair by fully encircling DNA as it sequentially hydrolyzes nucleotides - a biomolecular rotaxane The structure of the enzyme is shown in Fig. 3d. T4 DNA polymerase holoenzyme [38] is an analogous example its protein subunits clamp around a DNA strand to form a toroid in what chemists of the mechanical bond would call a clipping process. It should be noted that chemists have been able to mimic this concept of a topologically linked catalyst on a polymer [39] using traditional organic catalytic reactions. 

For DNA replication and repair, and for gene transcription, the DNA must be at least partially unwrapped. Unwrapping of the DNA involves an ATP-dependent disruption of nucleosomes and is part of gene transcription and a point of control. It allows transcriptional activators access to specific gene sites. Richmond s structure helps to Fig. 9.8 The nucleosome envisage how large enzyme complexes, such as the DNA... 

Dalrymple BP, Kongsuwan K, Wijffels G, Dixon NE, Jennings PA. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc. Natl. Acad. Sci. 2001 98 11627-11632. 

Rouse J, Jackson SP. LCDl an essential gene involved in checkpoint control and regulation of the MECl signalling pathway in Saccharomyces cerevisiae. EMBO J. 2000 19(21) 5801—5812. Weinert TA, Kiser GL, Hartwell LH. Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair. Genes Dev. 1994 8(6) 652—665. 

Tainer JA. Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 43. 2004 116 39-50. 

Reactions catalyzed by DNA gyrase within living bacteria include introduction of negative supertwists and the decatenation of interlocked circles and the consequent facilitation of DNA replication and repair. Quinolone agents act on this enzyme and cause inhibition of DNA synthesis, antagonism of RNA and protein synthesis and ultimately cell death. 

---