Aspects of bioorganic chemistry - a). Development of caffeine-aptamer for coffee decaffeination; b). Study of 1,8-naphthalimide derivatives as fluorescent probes; c). Encapsulation of DNA by silica nanoparticles

Research described in this thesis encompass three aspects of bioorganic chemistry: Caffeine- binding aptamers were sought to remove caffeine from coffee brew. Toward this goal, theophylline carboxylic acid and caffeine carboxylic acid were synthesized, and immobilized to ω-aminohexyl–agarose. The immobilized compounds were used for aptamer selection. The ionic composition of medium roast coffee grinds was determined by ICP-MS. In addition, the amounts of caffeine and theophylline in these brews were also determined by UV/vis and HPLC. The work described in this thesis provided the foundation for future aptamer selection. The development of 1,8-naphthalimide derivatives was motivated by an ability to stain biomolecules based on differences in their hydrophobicity. 1,8-naphthalimide derivatives were synthesized, and their photophysical and staining properties were investigated. The fluorescence intensity of 4-phenyl-1,8-naphthalimide was found to be very sensitive to solvent polarity, where the compound is virtually non-fluorescent in DMSO, large folds of fluorescence turn-on were seen in less polar solvents. Furthermore, this compound showed aggregation-induced emission characteristics. 4-Aryl-N-ethoxyethyl- and N-[2-(2-hydroxyethyoxy)ethoxy]ethyl-4-aryl-1,8-naphthalimide derivatives were also synthesized, with various aryl substituents (methoxy, amine, dimethyl amine, acetanilide). These compounds were found to be highly fluorescent in chloroform but were drastically reduced in DMSO and methanol. These dyes were found to be suitable probes for protein hydrophobicity, with up to 80 fold fluorescence turn on in the presence of BSA, but virtually no change in myoglobin. The thesis also explored the encapsulation of DNA by SNPs as an approach to protect DNA. Toward this goal, commercial SNPs were functionalized by the treatment with TMAPS and TEOS introducing a surface positive charge. Upon deposition of DNA to the positively charged surfaces, encapsulation was carried out by treatment with TMAPS and TEOS in the presence of ammonium hydroxide. This encapsulation protocol was first demonstrated using Reactive Green-19. In addition, DNA was readily encapsulated and released by the treatment with ammonium hydroxide at 60°C for six hours, and amplified by polymerase chain reaction and detected by gel electrophoresis. The SNP-encapsulated DNA was found to pass through beds of sand and could therefore be used in environmental tracking in sandy conditions.

Name thesis:degree_name

Ph.D. Biotechnology

Level thesis:degree_level

Doctoral

Discipline thesis:degree_discipline

Faculty of Mathematics and Science

Department dc:contributor.department

Centre for Biotechnology

Grantor

Brock University

Year dc:date.issued

2024

Author dc:creator

• Betancourt, Frank

• SNPs
• Decaffeination
• Aptamer
• Fluorescence
• Hydrophobicity probes

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/10464/18457

OAI identifier oai:identifier

oai:brocku.scholaris.ca:10464/18457