No description available.

No description available.

Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / We have constructed a database of hydroxyl radical (•OH) cleavage patterns of DNA in order to investigate the relationship between the sequence of a DNA molecule and its three-dimensional structure. The hydroxyl radical cuts DNA at every nucleotide, with the amount of cutting proportional to the solvent accessible surface area (SASA) of the deoxyribose hydrogen atoms. Cleavage fragments are quantified by a fluorescence sequencer, followed by normalization and deposition into the database. Our database currently contains 151 DNA sequences with lengths ranging from 35 to 41 nucleotides. These data have enabled us to develop some general rules regarding the sequence-dependence of DNA structure as well as to predict the cleavage pattern of any given DNA sequence with remarkable precision. Using this prediction algorithm, it is possible to construct structural maps of entire genomes. As there are many examples of DNA binding proteins with highly degenerate binding sites, the use of structural information to locate these sites may be helpful. There also exists other signals, including the signal for nucleosome positioning, which have no apparent consensus, making it likely that the structure of DNA is of critical importance. We have developed algorithms to identify regions of conserved structure using •OH cleavage intensity as a proxy. Within a set of DNase I hypersensitive sites (DHS) obtained from the ENCODE Consortium, we were able to identify a stretch of 12 nucleotides for which the structural conservation is much greater than the sequence conservation. These sites have been dubbed Conserved •OH Radical Cleavage Signatures, or CORCS. Upon further analysis, these CORCS were found to be 17-fold enriched for DHS as compared to shuffled elements. Through the continued analysis of hydroxyl radical cleavage data and development of algorithms to employ the data in biologically meaningful ways, we hope to further our understanding of the relationship between DNA sequence and structure, and how the local structural heterogeneity of genomic DNA contributes to biological function. / 2999-01-01

published_or_final_version / Chemistry / Master / Master of Philosophy

No description available.

The regioselectivity of the reaction of hydroxyl radical addition to toluene and naphthalene are examined in this study over the temperature range of 25°C-45°C. Also, the relative rates of reactivity as compared to benzene are determined for toluene, naphthalene, mesitylene, and p-xylene over the same temperature range. 2-(t-Butylazo)prop-2-yl hydroperoxide was used as the hydroxyl radical source and 1,1,3,3-tetramethylisoindolin-2-yloxyl was used as radical trap. For toluene the relative rates of addition were found to be 4 times greater for the ortho position versus the meta postion and 2 times greater for the para position versus the meta position, when the number of meta and para sites are taken into account. / Department of Chemistry

Hydroxyl radical HO plays a central role in controlling chemical processes in the troposphere. Current mechanisms are believed to accurately describe its formation, destruction and interaction with other atmospheric trace gases in clean air. Hydroperoxyl radical H0₂ is Iinked to HO in several chain processes and serves among other roles as a reservoir for HO. The relative concentration (H0₂/HO) in clean air is believed to be the order of 10². We here examine the conditions under which steady-state kinetics apply to HO₁ chemistry and derive simple relationships which can be used to predict HO and H0₂ concentration from measurable concentrations of the more stable trace gases. The equations assume a simple form for conditions where the ambient nitrogen oxide concentration is less than 1 ppb. These equations allow closed-form evaluation of the sensitivity of [HO] and [H0₂] to changes in the concentrations of the controlling species and allow assignment of uncertainty limits to the predictions of current tropospheric chemical models. Although most current efforts to test fast tropospheric photochemistry center upon measurements of ambient [HO], our equations indicate that tropospheric [H0₂] determinations may provide a more direct and accurate initial test of our knowledge of HO₁ chemistry in the unpolluted lower atmosphere. Overall the goal of this study is to benefit the experimenter by providing the information of insight and simple but reliable equations and to understand the conditions under which these measurements should be made and how best to interpret their results.

No description available.

published_or_final_version / Zoology / Master / Master of Philosophy

The work described in this thesis investigates the mechanisms by which copper complexes catalyse the generation of reactive oxygen species (ROS), including the highly reactive hydroxyl radical (.OH), and induce oxidative damage to DNA. An ESR study into the copper-Fenton reaction revealed that, in the presence of buffers and other copper chelators, .OH is generated. In contrast, it is suggested that a Cu(III) species may be formed in the reaction of aqueous, unchelated copper ions. The generation of .OH in the copper-Fenton reaction, under biomimetic conditions, was confirmed by analysis of the products formed following the incubation of DNA components with this system. Preferential binding of Cu(II) to guanosine over the other nucleosides was determined and copper redox cycling at GC sites was found to be more facile than at AT sites. Stability constants for the copper complexes with several other biochemically important ligands such as glutathione (GSH), Quin2 and 1,10-phenanthroline (OP) were also measured. The ease of redox cycling for the copper complexes was found to be of the order: OP ~ Quin2 > GSH. However, OP enhanced both the copper-Fenton reaction and copper-induced DNA damage while both GSH and Quin2 were inhibitory. Gel chromatography studies suggested that ternary complex formation occurs between Cu(I)-DNA and both Quin2 and OP. This implies that the ternary complex with OP is more redox active than that with Quin2. Whilst cysteine enhanced copper-mediated DNA damage at early incubation times, it was more protective than GSH and homocysteine at later stages. The effects at early incubation times are attributed to the ease of copper redox cycling in the presence of thiols while the effects over prolonged incubations reflect Cu(II) stabilisation by the respective disulphides or similar products.