Investigating Properties and Characteristics of G-quadruplex Structure, Folding, and Fluorescence
Open Access
- Author:
- Sherlock, Madeline Elizabeth
- Area of Honors:
- Chemistry
- Degree:
- Bachelor of Science
- Document Type:
- Thesis
- Thesis Supervisors:
- Philip C. Bevilacqua, Thesis Supervisor
Raymond Lee Funk, Thesis Honors Advisor
Scott A Showalter, Faculty Reader - Keywords:
- Nucleic Acids
RNA folding
G-Quadruplexes
Folding Cooperativity
Intrinsic fluorescence - Abstract:
- G-Quadruplex Structures (GQS) have been of recent interest due to their unique folding and spectroscopic properties, as well as their potential for target binding, modification for uses in sensing, and possible regulatory roles in vivo. This thesis explores all of these categories in both RNA and DNA G-Quadruplexes. GQSs with longer G-stretch length were developed to explore intermediates along the folding pathway and their effect on folding cooperativity to create a broadened response range for possible application in detection of analytes with highly variable concentrations. The recently-discovered intrinsic fluorescence of DNA GQSs was proven to also exist in RNA GQSs, which can be used as an alternative readout signal and could have potential for fluorescent imaging. This fluorescence was further characterized in DNA GQSs by systematic variation of the G-stretch length, loop nucleotides, and loop length. Effects on emission wavelength and signal intensity were observed and compared to high resolution structural data to better understand the nature of the GQS as a fluorophore. In order to further this understanding, the effects of dangling nucleotide ends and GQS concentration as well as varied conditions, such as Mg2+, temperature, quenchers, and crowding, were explored; the aim of these studies was increasing fluorescence signal toward the goal of developing an intrinsically fluorescent RNA for live cell imaging. Lastly, interactions of RNA GQSs with divalent metal ions were studied in the context of gene regulation by GQSs for heavy metal response with the finding of reversible unfolding by Cu2+ ions.