Correlation between physical and genetic maps of plasmids

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dc.contributor.advisorKlump, Horst Hen_ZA
dc.contributor.authorZubrzycki, Igor Zen_ZA
dc.date.accessioned2016-09-28T19:05:32Z
dc.date.available2016-09-28T19:05:32Z
dc.date.issued1992en_ZA
dc.description.abstractThe aim of this study is to establish a correlation between the physical maps of plasmid DNA (in the form of calorimetric profiles, thermal denaturation profiles and electron micrographs of partly melted DNA sequences) and genetic maps of these DNAs and thus deal with questions which were not answered by previous researchers. viz: Is there a correlation between base sequence function and a measurable physical property which can be assigned to biologically important units such as promoters or coding sequences? Is there a correlation between the denaturation of gene sequences and cooperative transitions observed in a given temperature interval? To answer these questions, a systematic study was initiated based on two families of plasmids with three different genes incorporated, namely the pGV 403 family which contains a Chloramphenicol resistance gene on one side and the pUC9 family which contains an Ampicillin and a Tetracycline resistance gene on the other side. Three different techniques were used to address the stated problems i.e. differential scanning calorimetry, high resolution thermal denaturation and electron microscopy. The reason for using three techniques instead of only one or two as in previous studies is that each technique gives specific results which can be supplemented by the other techniques and only in this way it will be possible to approach a deeper understanding of changes induced by perturbing the sequence based structural integrity by elevating temperature. In addition to measuring the experimentally observable parameters listed. a theoretical model was developed to predict the changes. This approach is termed local compositional complexity (LCC) analysis. The final goal of this investigation was to establish whether there is any correlation between the local compositional complexity and these selected genetic units. Based on the calorimetric experiments an improved table of thermodynamic data including the stacking energy for ten different combinations of basepairs is presented. The prediction of a melting curve based on primary structure information can be based on the enthalpy individual combination of basepairs[41.50.58]. The tables of the thermodynamic data published in the literature are given in Appendix D. In this thesis a slightly different approach to predict tm's was chosen (cf. p 67). The results obtained by this combined approach showed that there is indeed a correlation between the specific base sequence of a given plasmid DNA and its biologically important units (genes) and thus confirms that there is a semi-empirical correlation between genes and the observed cooperative melting units.en_ZA
dc.identifier.apacitationZubrzycki, I. Z. (1992). <i>Correlation between physical and genetic maps of plasmids</i>. (Thesis). University of Cape Town ,Faculty of Science ,Department of Molecular and Cell Biology. Retrieved from http://hdl.handle.net/11427/21986en_ZA
dc.identifier.chicagocitationZubrzycki, Igor Z. <i>"Correlation between physical and genetic maps of plasmids."</i> Thesis., University of Cape Town ,Faculty of Science ,Department of Molecular and Cell Biology, 1992. http://hdl.handle.net/11427/21986en_ZA
dc.identifier.citationZubrzycki, I. 1992. Correlation between physical and genetic maps of plasmids. University of Cape Town.en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Zubrzycki, Igor Z AB - The aim of this study is to establish a correlation between the physical maps of plasmid DNA (in the form of calorimetric profiles, thermal denaturation profiles and electron micrographs of partly melted DNA sequences) and genetic maps of these DNAs and thus deal with questions which were not answered by previous researchers. viz: Is there a correlation between base sequence function and a measurable physical property which can be assigned to biologically important units such as promoters or coding sequences? Is there a correlation between the denaturation of gene sequences and cooperative transitions observed in a given temperature interval? To answer these questions, a systematic study was initiated based on two families of plasmids with three different genes incorporated, namely the pGV 403 family which contains a Chloramphenicol resistance gene on one side and the pUC9 family which contains an Ampicillin and a Tetracycline resistance gene on the other side. Three different techniques were used to address the stated problems i.e. differential scanning calorimetry, high resolution thermal denaturation and electron microscopy. The reason for using three techniques instead of only one or two as in previous studies is that each technique gives specific results which can be supplemented by the other techniques and only in this way it will be possible to approach a deeper understanding of changes induced by perturbing the sequence based structural integrity by elevating temperature. In addition to measuring the experimentally observable parameters listed. a theoretical model was developed to predict the changes. This approach is termed local compositional complexity (LCC) analysis. The final goal of this investigation was to establish whether there is any correlation between the local compositional complexity and these selected genetic units. Based on the calorimetric experiments an improved table of thermodynamic data including the stacking energy for ten different combinations of basepairs is presented. The prediction of a melting curve based on primary structure information can be based on the enthalpy individual combination of basepairs[41.50.58]. The tables of the thermodynamic data published in the literature are given in Appendix D. In this thesis a slightly different approach to predict tm's was chosen (cf. p 67). The results obtained by this combined approach showed that there is indeed a correlation between the specific base sequence of a given plasmid DNA and its biologically important units (genes) and thus confirms that there is a semi-empirical correlation between genes and the observed cooperative melting units. DA - 1992 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PB - University of Cape Town PY - 1992 T1 - Correlation between physical and genetic maps of plasmids TI - Correlation between physical and genetic maps of plasmids UR - http://hdl.handle.net/11427/21986 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/21986
dc.identifier.vancouvercitationZubrzycki IZ. Correlation between physical and genetic maps of plasmids. [Thesis]. University of Cape Town ,Faculty of Science ,Department of Molecular and Cell Biology, 1992 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/21986en_ZA
dc.language.isoengen_ZA
dc.publisher.departmentDepartment of Molecular and Cell Biologyen_ZA
dc.publisher.facultyFaculty of Scienceen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.subject.otherBiochemistryen_ZA
dc.titleCorrelation between physical and genetic maps of plasmidsen_ZA
dc.typeDoctoral Thesis
dc.type.qualificationlevelDoctoral
dc.type.qualificationnamePhDen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceThesisen_ZA
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