Escherichia coli MutS is a DNA binding repair protein (97 kDa, monomer) and its biological significance arises from its recognition of mismatches which occur as errors during DNA replication. Mismatches and mutagenic bases represent a fascinating and diverse range of shapes and sizes and it is not obvious how a single protein (MutS) can recognise such molecular diversity against a huge background of canonical Watson-Crick base pairs. In this project, the structure of a 17mer mismatch GT DNA was carried out using NMR spectroscopy to identify the differences caused by the introduction of a non-canonical base pair on helical structure. The resulting structure was B-form in conformation and local helical distortions were observed about the GT mispair due primarily to its sheared orientation. The effect of mismatch orientation, sequence context and oligonucleotide length on mismatch stability was also investigated using UV absorbance melting and NMR spectroscopy. The results showed that substitution of a TG mispair for a GT mispair was accompanied by a small drop in melting temperature. It was also discovered that sequences in which purine-purine or pyrimidine-pyrimidine stacking occurred induced additional stability of the mismatch resulting in a higher melting temperature of the duplex.Affinity of mismatch GT DNA and its mismatch orientation, sequence context and length analogues for MutS was investigated by monitoring changes to the chemical shifts and linewidths of imino protons resonances during NMR titration. The results showed that MutS displayed higher affinity towards sequences which involved better stacking between the flanking base pairs and the GT/TG mispair.Analogous NMR structural investigations of 6-thioguanine modified 13mer GC DNA and its oxidised derivatives have been successfully carried out. The NMR structure was successfully determined of the former and the results obtained showed the effect on helical structure induced by the substitution of a different DNA lesion.Although the crystal structures of MutS bound to DNA mismatches have been known for a number of years, the analogous crystal structures of uncomplexed apo MutS have not been determined to date. Consequently, vital structural knowledge on the large change in conformation of MutS upon binding to the DNA mismatch is seriously lacking. We have successfully isolated the structurally and functionally important NTD of E. coli MutS and its labelled (13C, 15N) analogues and have shown that it is endowed with a stable, tertiary structural fold and well suited to NMR structure determination. This is exemplified by the assignments of several backbone amide and side chain resonances using isotope aided 3D NMR techniques.

The von Hippel-Lindau (VHL) tumor suppressor pVHL is lost in 90% of clear-cell renal-cell carcinomas (ccRCCs). Jade-1 is a renal tumor suppressor that is normally stabilized by pVHL. MutS Homolog2 (MSH2) is a key initiator in DNA mismatch repair (MMR). Defects in MMR are associated with genome-wide instability and predisposition to certain types of cancer. Mass spectrometry data of immunoprecipitated Flag-tagged Jade-1 lysates showed signal for MSH2, suggesting Jade-1 may participate in MMR. Here, we confirmed an interaction between endogenous MSH2 and endogenous Jade-1 by coimmunoprecipitation. Using cell fractionation, we found that MSH2 and Jade-1 translocated to the nucleus in response to alkylating agent MNNG in kidney proximal tubule cells. We also visualized the translocation of Jade-1 by immunofluorescence. Silencing JADE1 also influenced the kinetics of MSH2 translocation. In addition, by colony forming assay, JADE1-silenced cells were resistant to mismatch damage induced by MNNG, which is a feature of cells with an MMR defect. Furthermore, reintroducing pVHL into renal cancer cells also changed the amount of translocated MSH2 and Jade-1. In contrast to wild-type mice, Jade1 heterozygous mice got spontaneous tumors, and those tumors continued to show heterozygosity for Jade1. Taken together, our results identify a mechanism for Jade-1 regulation of MMR through its nuclear translocation. pVHL may also contribute to MSH2 and Jade-1 translocation by increasing Jade-1 abundance. These findings establish an early role for Jade-1 in MMR, provide further indication that Jade-1 helps maintain genomic stability in the kidney and support that Jade-1 is a haploinsufficient renal tumor suppressor.

The DNA Mismatch repair (MMR) pathway is responsible for the repair of base-base mismatches and insertion/deletion loops that arise during DNA replication. MMR deficiency is currently estimated to be present in 15-17% of colorectal cancer cases and 30% of endometrial cancers. MLH1 is one of the key proteins involved in the MMR pathway. MMR deficient tumours are often resistant to standard chemotherapies, therefore there is a critical need to identify new therapeutic strategies to treat MMR deficient disease. This study demonstrates that MLH1 deficient tumours are synthetically lethal with the mitochondrial-targeted agent Parthenolide which is known to induce reactive oxygen species (ROS) as one of its main mechanisms of action. Upon functional analysis, I show for the first time that loss of MLH1 is associated with deregulated mitochondrial function evidenced by a reduction in complex I expression and activity, reduced basal oxygen consumption rate and reduced spare respiratory capacity. This mitochondrial phenotype in the MLH1-deficient cell lines is accompanied by a reduction in mitochondrial biogenesis as evidenced by down regulation of pgc1β and decreased mitochondrial copy number. Furthermore, MLH1-deficient cancer cells have a decreased antioxidant defence capacity with reduced expression of the antioxidant genes NRF1, NRF2, Catalase, Glutathione peroxidase and SOD1 as well as increased ROS production when treated with Parthenolide. I further demonstrate that both MSH2- and MSH6-deficient cell lines also display deficiencies in complex I compared to their MMR-proficient counterparts. Taken together, the results of this study show a novel role for MLH1 in mitochondrial function and biogenesis. The MMR proteins MSH2 and MSH6 are also likely to have a role in the mitochondria. My results suggest that targeting the mitochondria may be a potential therapeutic strategy for the treatment of MMR and specifically MLH1 deficient disease.

Thesis (M.S.)--University of Toledo, 2007. / "In partial fulfillment of the requirements for the degree of Master of Science in Biomedical Sciences." Title from title page of PDF document. Bibliography: p. 50-55.

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 132-147).

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 56-75).

Maintaining genomic integrity is important for any organism. DNA mismatch repair (MMR) serves to correct errors that occur during DNA replication and recombination, such as unpaired bases or mismatched bases. Mutl is a key player and serves to coordinate protein-protein interactions. Recently it has been shown that human Mutl functions as an endonuclease and that this activity is imperative for functioning MMR. In this work, the X-ray crystal structure of the C-terminal endonuclease domain of Bacillus subtilis Mutl (BsMutL-CTD) is presented. Diffraction quality crystals of BsMutL-CTD were grown using vapor diffusion. The crystal structure of BsMutL-CTD was solved using multiwavelength anomalous diffraction. The structure reveals a putative metal binding site which clusters closely in space with endonuclease motif. Using the structure and sequence homology, several mutations were made and an investigation into the endonuclease activity of BsMutL was performed. BsMutL was confirmed to be a manganese-dependent endonuclease and key residues which contribute to endonuclease function were identified. / Thesis / Master of Science (MSc)

Yes / Temozolomide (TMZ) is the standard first line treatment for malignant glioma, reaching “blockbuster” status in 2010, yet it remains the only drug in its class. The main constraints on the clinical effectiveness of TMZ therapy are its requirement for active DNA mismatch repair (MMR) proteins for activity, and inherent resistance through O6-methyl guanine-DNA methyl transferase (MGMT) activity. Moreover, acquired resistance, due to MMR mutation, results in aggressive TMZ-resistant tumour regrowth following good initial responses. Much of the attraction in TMZ as a drug lies in its PK/PD properties: it is acid stable and has 100% oral bioavailability; it also has excellent distribution properties, crosses the blood-brain barrier, and there is direct evidence of tumour localisation. This review seeks to unravel some of the mysteries of the imidazotetrazine class of compounds to which TMZ belongs. In addition to an overview of different synthetic strategies, we explore the somewhat unusual chemical reactivity of the imidazotetrazines, probing their mechanisms of reaction, examining which attributes are required for an active drug molecule and reviewing the use of this combined knowledge towards the development of new and improved anti-cancer agents.

The DNA Mismatch repair (MMR) pathway is responsible for the repair of base-base mismatches and insertion/deletion loops, formed during DNA replication. Mutations in MMR genes significantly increase the predisposition to cancer with MMR deficiency estimated to be present in 15-17 % of all colorectal cancers. 5-fluorouracil is the main treatment for advanced colorectal cancer however the majority of studies suggest that MMR deficient tumours are more resistant to 5-fluorouracil than MMR proficient tumours. Therefore, there is a critical clinical need to identify novel therapeutics to treat these tumours. To this end, we have performed a high-throughput compound screen, to identify compounds that cause selective lethality in MMR deficient cell lines. We identified the potassium-sparing diuretic drug, Triamterene, as selectively lethal in vitro and in vivo in MMR deficient cell lines. Our data suggest that this selectivity is through its antifolate activity, leading to the accumulation of reactive oxygen species and DNA double strand breaks in MMR deficient cells. Interestingly, we identified a requirement, for thymidylate synthase expression, the only de novo enzyme for dTTP synthesis for the Triamterene cytotoxicity. NRF2 and NRF2-induced antioxidants were regulated upon Triamterene treatment and thymidylate synthase silencing, therefore suggesting a role for the antioxidant response in Triamterene toxicity. Taken together, our results suggest Triamterene as a promising novel therapeutic for the treatment of MMR deficient cancers. In order to identify novel therapeutics to treat MMR deficient tumours, we have also performed a high-throughput siRNA screen, to identify genes that cause selective lethality in MMR deficient cell lines. We identified AURKA gene as synthetically lethal in MSH6 deficient cell lines which suggests AURKA as a promising novel therapeutic target for the treatment of MMR deficient cancers. Taken together, in this PhD thesis we have identified two novel therapeutic strategies for the treatment of MMR deficient cancers.

PCNA and RPA are required for DNA mismatch repair (MMR), but their rolesin the pathway are not fully understood. Using an affinity pull-down approach, weshow that (1) increased PCNA binding to DNA heteroduplexes is associated withthe appearance and accumulation of excision products; and (2) RPAphosphorylation occurs when DNA polymerase ?? binds to the DNA substrate. Wetherefore hypothesize that PCNA plays an important role in mismatch-provokedexcision and that RPA phosphorylation plays an important role in DNA resynthesis.To determine the role of PCNA in MMR, mismatch-provoked and nick-directedexcision was assayed in a cell-free system in the presence of the PCNA inhibitor,p21CIP1/WAF. We show that whereas PCNA is essential for 3' directed excision, it isdispensable for the 5' directed reaction, suggesting a differential role for PCNA inMMR. We further find that the PCNA-dependent pathway is the only pathway for3' directed excision, but there are at least two pathways for 5' directed excision,one of which is a PCNA-independent 5' excision pathway. To determine if RPAphosphorylation facilitates DNA resynthesis, a gap-filling assay was developedusing both a cell-free system and a purified system, and we demonstrate that RPAphosphorylation stimulates DNA polymerase ??-catalyzed resynthesis in bothsystems. Kinetic studies indicate that phosphorylated RPA has a lower affinity forDNA compared with un-phosphorylated RPA. Therefore, the stimulation ofresynthesis by phosphorylated RPA is likely due to the fact that phosphorylationpromotes the release of RPA from DNA, thereby making DNA template availablefor resynthesis.