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The in vivo synthesis of deoxyribonucleic acid from labeled precursors was studied in the rat intestinal mucosa in an attempt to elucidate the complex process of DNA replication. In one set of experiments, the rats were injected with ³H-thymidine and then starved for 24 hours, in which time the stable DNA became labelled with tritium. (14)C-thymidine was then administered and the animals were sacrificed 5 minutes later. By this procedure the newly synthesized DNA was labelled with (14)C. The DNA, was fractionated by chromatography on a methylated-albumin kieselguhr column. Only one main peak of DNA was eluted with a sodium chloride solution ranging in concentration from 0.5-0.6 M. The thermal denaturation temperature for the DNA in each.fraction from this peak was determined and the G + C content was calculated:, Within the DNA peak obtained from MAK chromatography, the G + C content of the DNA decreased with increasing fraction number. In addition to these differences in base composition, there were differences in metabolic activity between the fractions, which were indicated by their ³H/ (14)C ratios. The ³H/ (14)C ratio of the DNA fractions from MAK chromatography increased with fraction number to a maximum at fraction 4 or 5 and then decreased. It was found that the ³H/O.D. ratio of the fractions was not constant, thus suggesting that the tritium might be unevenly distributed throughout the fractions. If the time interval between the ³H and (14)C-thymidine injections was reduced to 3 ½ hours, the ³H/O.D. ratio became constant while the pattern of the ³H/14C ratios remained unchanged. If (14)C-thymidine was administered 20 minutes before the animals were sacrificed, the ³H/(14)C ratio of the DNA fractions from MAK chromatography increased with increasing fraction number. From these results it was concluded that small molecular weight, newly synthesized DNA, which was highly labelled with (14)C, was being incorporated with time into the high molecular weight, stable DNA fraction, which is labelled with ³H. During these experiments it was observed that the pattern of ³H/(14)C ratio versus fraction number varied according to the treatment given to the DNA sample prior to the preparation for radioactive counting. If the sample was denatured by heating to obtain its T(M) value, and then dialyzed against distilled water, small molecular weight nucleotides passed into the dialysate. The denatured DNA sample also gave different results from the native DNA sample on digestion with snake venom phosphodiesterase. On the denatured sample, the pattern of release of ³H and (14)C labelled material into the acid soluble material, indicated that both these labels were uniformly distributed along the DNA chain. On the other hand, with the native 5 min. DNA samples, the release of (14)C labelled material into the acid soluble fraction was that expected for DNA which had incorporated (14)C-preferentially into the 3’ terminal positions. The separation of the pyrimidine clusters of DNA indicated that those were not uniformly labelled with (14)C and ³H. / Medicine, Faculty of / Biochemistry and Molecular Biology, Department of / Graduate

Bacteria regulate gene expression through coordinated interactions between cis-regulatory sequences and trans-regulatory factors. Understanding the molecular basis for the functions of these regulatory components is not only essential for deciphering complex biological processes in diverse bacteria but also critical for rational engineering of microbial phenotypes. However, systematically dissecting the sequence-function relationships of cis and trans regulatory components that underly gene expression is still a key challenge. Recent technological advances have provided novel tools and methods for mapping sequence-function relationships in high-throughput. This dissertation focuses on applying novel methods enabled through increased throughput and scalability of DNA synthesis and sequencing to elucidate the sequence-function relationships of cis and trans components that underlie bacterial gene regulation. In Chapter 2, evolutionary and functional diversity of primary σ70, a universally conserved global regulator in bacteria, is studied through comparative genomics, saturation mutagenesis, and transcriptomics. Through the combined efforts of these approaches, we demonstrate that sequence diversity of σ70 factors reflects functional differences which have been shaped by evolutionary constraints from co-evolving regulatory sequence targets during evolution. Chapter 3 discusses systematically mapping transcriptional activities of cis-regulatory sequences from Biosynthetic Gene Clusters (BGCs). Using a Streptomyces as a host, we found key regulatory features that affected gene expression, such as GC content, transcription start sites, and sequence motifs. We further explored regulation of BGC derived regulatory sequences by expressing global regulatory factors and screening for regulator sequences with altered expression levels. Finally, Chapter 4 highlights recent studies that made key contributions towards elucidating and modulating bacterial gene regulatory networks and reviews the current state of microbial systems biology and gene regulation. Together, the results and discussions presented in this dissertation seeks to further advance the current knowledge of sequence-function relationships of microbial regulatory components to enable better understanding, modeling, and rational engineering of bacterial gene regulation.

No description available.

The effect on DNA repair in ultraviolet-irradiated human skin fibroblasts by hydroxyurea has been examined in this study using three independent methods for measuring DNA repair: the 5-bromodeoxyuridine photolysis assay which measures DNA repair replication, chromatographic measurement of thymine-containing dimers, and measurement of specific ultraviolet-endonucleasesensitive sites in irradiated DNA. Little effect of hydroxyurea was observed at the concentration of 2 mM, which is often used to inhibit semiconservative DNA synthesis; however, 10 mM hydroxyurea resulted in marked inhibition (65-70%) of excision repair. This inhibition was accompanied by a possible doubling in the size of the repaired region. The accumulation of large numbers of single-strand breaks following ultraviolet irradiation and hydroxyurea incubation seen by other investigators was not observed with the normal skin fibroblasts used in this study. A comparison of hydroxyurea effects on the different DNA repair assays indicates inhibition of one step in DNA repair also results in varying degrees of inhibition of other steps as well.

Indiana University-Purdue University Indianapolis (IUPUI) / The DNA minor groove continues to be an important biological target in the development of anticancer, antiviral, and antimicrobial compounds. Among agents that target the minor groove, studies of well-established benzimidazole-based DNA binders such as Hoechst 33258 have made it clear that the benzimidazole-amidine portion of these molecules promotes an efficient, site-selective DNA association. Building on the beneficial attributes of existing benzimidazole-based DNA binding agents, a series of benzimidazole-amino acid conjugates was synthesized to investigate their DNA recognition and binding properties. In this series of compounds, the benzimidazole-amidine moiety was utilized as a core DNA “anchoring” element accompanied by different amino acids to provide structural diversity that may influence DNA binding affinity and site-selectivity. Single amino acid conjugates of benzimidazole-amidines were synthesized, as well as a series of conjugates containing 20 dipeptides with the general structure Xaa-Gly. These conjugates were synthesized through a solid-phase synthetic route building from a resin-bound amino acid (or dipeptide). The synthetic steps involved: (1) the coupling of 4-formylbenzoic acid to the resin-bound amino acid (via diisopropylcarbodiimide and hydroxybenzotriazole); followed by (2) introduction of a 3,4-diaminobenzamidoxime in the presence of 1,4-benzoquinone to construct the benzimidazole ring; and, finally, (3) reduction of the resin-bound amidoxime functionality to an amidine via treatment with 1M SnCl2•2H2O in DMF before cleavage of final product from the resin. The synthetic route developed and employed was simple and straightforward except for the final reduction that proved to be very arduous. All target compounds were obtained in good yield (based upon weight), averaging 73% mono-amino acid and 78% di-amino acid final compound upon cleavage from resin. Ultimately, the DNA binding activities of the amino acid-benzimidazole-amidine conjugates were analyzed using a fluorescent intercalator displacement (FID) assay and calf thymus DNA as a substrate. The relative DNA binding affinities of both the mono- and di-amino acid-benzimidazole-amidine conjugates were generally weaker than that of netropsin and distamycin with the dipeptide conjugates showing stronger binding affinities than the mono-amino acid conjugates. The dipeptide conjugates containing amino acids with positively charged side chains, Lys-Gly-BI-(+) and Arg-Gly-BI-(+), showed the strongest DNA binding affinities amongst all our synthesized conjugates.

This investigation addresses the interrelated problems of A) Uptake and vascular transport of lipophilic chemical carcinogens, and intracellular interactions between lipoproteins and carcinogens; B) Biochemical mechanisms by which polynuclear aromatic hydrocarbon carcinogens inhibit the replicative and repair DNA synthesis in cells. The results observed in this study suggest that ingested benzo(a)pyrene (BaP) enters the gastrointestinal lymphatic drainage sequestered within lymphatic lipoproteins, and that low-density lipoproteins (LDL) play a major role in the vascular transport of BaP. BaP is taken up into cells by adsorptive endocytosis mediated by an interaction between apolipoprotein-specific receptors on the cell membrane and the specific apolipoproteins on LDL. Having entered peripheral cells sequestered within the lipid core of LDL, an electrophilic metabolite of BaP covalently binds to cellular DNA, and may interact with other cellular macro-molecules. Data presented here suggest that LDL is also absolutely required for the activation of DNA polymerase-a, which is the major enzyme of DNA excision repair necessary to correct the DNA damage caused by BaP. This study concludes that an active metabolite of the polynuclear aromatic hydrocarbon carcinogen, benzo(a)pyrene, suppresses DNA polymerase-a activity by inhibiting the binding of 2'-deoxyguanosine 5'-triphosphate to an acceptor site on the DNA polymerase-a complex with the DNA substrate, thereby competitively inhibiting interaction of 2'-deoxyguanosine 5'-triphosphate in the DNA synthetic process.

Forensic STR analysis is limited by the quality and quantity of DNA. Significant damage or alteration to the molecular structure of DNA by depurination, crosslinking, base modification, and strand breakage can impact typing success. Two methods that could potentially improve STR typing of challenged samples were explored: an in vitro DNA repair assay (PreCR™ Repair Mix) and whole genome amplification. Results with the repair assay showed trends of improved performance of STR profiling of bleach-damaged DNA. However, the repair assay did not improve DNA profiles from environmentally-damaged bloodstains or bone, and in some cases resulted in lower RFU values for STR alleles. The extensive spectrum of DNA damage and myriad combinations of lesions that can be present in forensic samples appears to pose a challenge for the in vitro PreCR™ assay. The data suggest that the use of PreCR™ in casework should be considered with caution due to the assay’s varied results. As an alternative to repair, whole genome amplification (WGA) was pursued. The DOP-PCR method was selected for WGA because of initial primer design and greater efficacy for amplifying degraded samples. Several modifications of the original DOP-PCR primer were evaluated. These modifications allowed for an overall more robust amplification of damaged DNA from both contemporary and historical skeletal remains compared with that obtained by standard DNA typing and a previously described DOP-PCR method. These new DOP-PCR primers show promise for WGA of degraded DNA.

Standard chemical DNA synthesis with isotope labels requires expensive reagents; moreover, a large excess of phosphoramadites (typically 50-100 fold) must be used. We developed a process where enzymatic cyclic solid phase synthesis of DNA allows for more economic reagent use. A DNA template was immobilized on an epoxy-activated solid support. This chemistry was chosen because the formed linkage is inert to high pH conditions. High efficiency of the covalent attachment was observed when the reaction was carried out in MgCl2/CAPS buffer. It was found that Mg2+ enables the reaction to be completed over a period of 14 h, compared to 72 h under standard conditions. DNA synthesis was carried in a cyclic fashion on a support bound DNA using Klenow fragment.

Bibliography: leaves 267-287 / xviii, 287, [ca. 40] leaves, [10] leaves of plates : ill ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Biochemistry, 1985