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Correlation between physical and genetic maps of plasmids
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 answer...
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| Format: | Thesis |
| Language: | English |
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Department of Molecular and Cell Biology
2016
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| _version_ | 1867614367500992512 |
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| access_status_str | Open Access |
| author | Zubrzycki, Igor Z |
| author2 | Klump, Horst H |
| author_browse | Klump, Horst H Zubrzycki, Igor Z |
| author_facet | Klump, Horst H Zubrzycki, Igor Z |
| author_sort | Zubrzycki, Igor Z |
| collection | Thesis |
| description | 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. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/21986 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:50:55.237Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Department of Molecular and Cell Biology |
| publisherStr | Department of Molecular and Cell Biology |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/21986 Correlation between physical and genetic maps of plasmids Zubrzycki, Igor Z Klump, Horst H Biochemistry 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. 2016-09-28T19:05:32Z 2016-09-28T19:05:32Z 1992 Doctoral Thesis Doctoral PhD http://hdl.handle.net/11427/21986 eng application/pdf Department of Molecular and Cell Biology Faculty of Science University of Cape Town |
| spellingShingle | Biochemistry Zubrzycki, Igor Z Correlation between physical and genetic maps of plasmids |
| thesis_degree_str | Doctoral |
| title | Correlation between physical and genetic maps of plasmids |
| title_full | Correlation between physical and genetic maps of plasmids |
| title_fullStr | Correlation between physical and genetic maps of plasmids |
| title_full_unstemmed | Correlation between physical and genetic maps of plasmids |
| title_short | Correlation between physical and genetic maps of plasmids |
| title_sort | correlation between physical and genetic maps of plasmids |
| topic | Biochemistry |
| url | http://hdl.handle.net/11427/21986 |
| work_keys_str_mv | AT zubrzyckiigorz correlationbetweenphysicalandgeneticmapsofplasmids |