Bacteriorhodopsin (bR) is a highly expressed transmembrane protein that acts as a light-driven proton pump converting light energy into a proton gradient. The extraordinary levels of expression achieved (15-30 mg per liter of culture) are a result of very efficient biogenesis that originates from molecular information encoded in the bacterio-opsin gene {bop) (1). DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a \"stem-loop\"). Using biophysical methods, the goal was to determine if the stem-loop structure exists in solution conditions that mimic the in vivo biological environment (42°C and 4M KCl) (2-4). The salt-dependent thermal stability of a DNA model of the stem-loop sequence was obtained using temperature-controlled UVabsorption and Circular Dichroism (CD) spectroscopy and Differential Scanning Calorimetry (DSC). The combinatorial analysis indicates that an energetically favorable stem-loop structure forms in all solution conditions examined. The stem-loop structure is stabilized at very high salt concentrations, a requirement for a role in bop gene expressivity (AG= -1.13 kcal/mol, AH= -16.78 kcal/mol, AS= - 49.67 cal/mol/K). While the Tm values evaluated by all three physical techniques were comparable, comparison of the calorimetrie and van't Hoff enthalpies indicate that the folding mechanism is not a two-state process. SVD analysis of the UV and CD spectral transitions confirm that formation of the stem-loop structure proceeds through a single significant folding intermediate. Similar analysis of the RNA sequence demonstrates that an RNA stem- loop structure can form and is significantly more stable than that of the DNA structure at all salt concentrations evaluated.
","abstract_html":"<p>Bacteriorhodopsin (bR) is a highly expressed transmembrane protein that acts as a light-driven proton pump converting light energy into a proton gradient. The extraordinary levels of expression achieved (15-30 mg per liter of culture) are a result of very efficient biogenesis that originates from molecular information encoded in the bacterio-opsin gene {bop) (1). DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a "stem-loop"). Using biophysical methods, the goal was to determine if the stem-loop structure exists in solution conditions that mimic the in vivo biological environment (42°C and 4M KCl) (2-4). The salt-dependent thermal stability of a DNA model of the stem-loop sequence was obtained using temperature-controlled UVabsorption and Circular Dichroism (CD) spectroscopy and Differential Scanning Calorimetry (DSC). The combinatorial analysis indicates that an energetically favorable stem-loop structure forms in all solution conditions examined. The stem-loop structure is stabilized at very high salt concentrations, a requirement for a role in bop gene expressivity (AG= -1.13 kcal/mol, AH= -16.78 kcal/mol, AS= - 49.67 cal/mol/K). While the Tm values evaluated by all three physical techniques were comparable, comparison of the calorimetrie and van't Hoff enthalpies indicate that the folding mechanism is not a two-state process. SVD analysis of the UV and CD spectral transitions confirm that formation of the stem-loop structure proceeds through a single significant folding intermediate. Similar analysis of the RNA sequence demonstrates that an RNA stem- loop structure can form and is significantly more stable than that of the DNA structure at all salt concentrations evaluated.</p>","abstract_has_math":false,"creators":["Darwish, Maged A"],"institution":null,"degree_name":"PhD. Chemistry","degree_level":"Dissertation","degree_discipline":"Chemistry and Biochemistry","degree_department":null,"school":null,"contributors":["Stephen P. Kelty","Cecilia H. Marzabadi","Wyatt R. Murphy","Cosimo Antonacci","George J. Turner"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2010,"date_issued":"2010-01-01T08:00:00Z","date_published":"2010-01-01T08:00:00Z","updated_at":"2026-07-24T04:32:12Z","subjects":["Pure sciences","Nucleic acids","Secondary structures","Gene expression","Biochemistry"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://scholarship.shu.edu/dissertations/1435","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Stephen P. Kelty","Cecilia H. Marzabadi","Wyatt R. Murphy","Cosimo Antonacci","George J. 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DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a \"stem-loop\"). Using biophysical methods, the goal was to determine if the stem-loop structure exists in solution conditions that mimic the in vivo biological environment (42°C and 4M KCl) (2-4). The salt-dependent thermal stability of a DNA model of the stem-loop sequence was obtained using temperature-controlled UVabsorption and Circular Dichroism (CD) spectroscopy and Differential Scanning Calorimetry (DSC). The combinatorial analysis indicates that an energetically favorable stem-loop structure forms in all solution conditions examined. The stem-loop structure is stabilized at very high salt concentrations, a requirement for a role in bop gene expressivity (AG= -1.13 kcal/mol, AH= -16.78 kcal/mol, AS= - 49.67 cal/mol/K). While the Tm values evaluated by all three physical techniques were comparable, comparison of the calorimetrie and van't Hoff enthalpies indicate that the folding mechanism is not a two-state process. SVD analysis of the UV and CD spectral transitions confirm that formation of the stem-loop structure proceeds through a single significant folding intermediate. Similar analysis of the RNA sequence demonstrates that an RNA stem- loop structure can form and is significantly more stable than that of the DNA structure at all salt concentrations evaluated.
"]},{"key":"dc:title","label":"Title","values":["Stability of Nucleic Acid Secondary Structures and Their Contribution to Gene Expression"]}]}],"canonical_facts":{"dc:contributor":["Stephen P. Kelty","Cecilia H. Marzabadi","Wyatt R. Murphy","Cosimo Antonacci","George J. Turner"],"dc:creator":["Darwish, Maged A"],"dc:date.available":["2011-10-04T07:00:00Z"],"dc:description.abstract":["Bacteriorhodopsin (bR) is a highly expressed transmembrane protein that acts as a light-driven proton pump converting light energy into a proton gradient. The extraordinary levels of expression achieved (15-30 mg per liter of culture) are a result of very efficient biogenesis that originates from molecular information encoded in the bacterio-opsin gene {bop) (1). DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a \"stem-loop\"). Using biophysical methods, the goal was to determine if the stem-loop structure exists in solution conditions that mimic the in vivo biological environment (42°C and 4M KCl) (2-4). The salt-dependent thermal stability of a DNA model of the stem-loop sequence was obtained using temperature-controlled UVabsorption and Circular Dichroism (CD) spectroscopy and Differential Scanning Calorimetry (DSC). The combinatorial analysis indicates that an energetically favorable stem-loop structure forms in all solution conditions examined. The stem-loop structure is stabilized at very high salt concentrations, a requirement for a role in bop gene expressivity (AG= -1.13 kcal/mol, AH= -16.78 kcal/mol, AS= - 49.67 cal/mol/K). While the Tm values evaluated by all three physical techniques were comparable, comparison of the calorimetrie and van't Hoff enthalpies indicate that the folding mechanism is not a two-state process. SVD analysis of the UV and CD spectral transitions confirm that formation of the stem-loop structure proceeds through a single significant folding intermediate. Similar analysis of the RNA sequence demonstrates that an RNA stem- loop structure can form and is significantly more stable than that of the DNA structure at all salt concentrations evaluated.
"],"dc:identifier":["https://scholarship.shu.edu/dissertations/1435"],"dc:subject":["Pure sciences","Nucleic acids","Secondary structures","Gene expression","Biochemistry"],"dc:title":["Stability of Nucleic Acid Secondary Structures and Their Contribution to Gene Expression"],"thesis:degree_discipline":["Chemistry and Biochemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["PhD. Chemistry"]},"updated_at":"2026-07-24T04:32:12Z"}