Hybridization Kinetics of Four-Way Junctions Localized on a DNA Scaffold

Author

Katherine N. Taylor, University of Central FloridaFollow

Keywords

DNA, nanotechnology, biochemistry, hybridization, kinetics, four-way junctions

Abstract

DNA computing is an ever-growing field with scientists trying to design structures that optimize logic gate communication to develop fast, biologically compatible, computational structures. We hypothesize that by using the principles of DNA computing, it is possible to design a DNA tile capable of studying localized DNA hybridization that can differentiate between oligonucleotides of different structural conformations. This includes synthetically manipulating DNA into a nanostructure that can perform Boolean logic functions to calculate the different rates of hybridization. To test our hypothesis, we designed a DNA Tile that incorporated a 4WJ using YES logic. Linear and hairpin single-stranded (ss) DNA varieties complimentary to the DNA Tile were added in solution and monitored on their hybridization with the structure, using a fluorophore/quencher reporter system. These kinetic studies showed that the linear strand hybridized faster to the DNA Tile than the hairpin structures, demonstrating that faster association was accomplished with uninhibited strands instead of self-inhibited strands. In addition, the DNA tile was able to differentiate the different hybridization rates of self-inhibited strands in relation to their stem length.

Thesis Completion Year

2024

Thesis Completion Semester

Spring

Thesis Chair

Kolpashchikov, Dmitry

College

College of Sciences

Department

Chemistry

Thesis Discipline

Biochemistry

Language

English

Access Status

Open Access

Length of Campus Access

None

Campus Location

Orlando (Main) Campus

STARS Citation

Taylor, Katherine N., "Hybridization Kinetics of Four-Way Junctions Localized on a DNA Scaffold" (2024). Honors Undergraduate Theses. 128.
https://stars.library.ucf.edu/hut2024/128