Theoretical analysis of DNA bridge-mediated electron transfer (ET) led to the proposal that photoinduced ET might occur via either superexchange or hopping mechanisms. Electron transfer has been proposed to occur via a superexchange mechanism at short distances and via a hopping mechanism at longer distances. However, a crossover in mechanism has not been directly observed for photoinduced charge transfer in DNA. Using multiple spectroscopic techniques, a detailed analysis of the formation and decay of the stilbene acceptor singlet state and of the charge separated intermediates has been carried out for synthetic DNA hairpins possessing donor and acceptor stilbenes. Studies have shown that the superexchange mechanism is adopted at short bridge distance (R≈10 Ǻ), while the hole hopping mechanism is dominant when the number of intervening base pairs is three or more. The charge separation, and charge recombination processes are distance dependent, whereas the hole injection and hole trapping are only dependent upon their energetics. Hole migration rates estimated from hole arrival times indicate a low hole mobility in DNA A-tracts. Tri- or hexa- ethyleneglycol linked hairpins have been designed to prevent competitive absorption from natural nucleobases and chromophoric linkers. The thermal stability studies show both linkers can construct stable hairpins as short as 5 base pairs. The length of the linkers determine the thermal stability of constructed hairpins due to the impact on base pairing conformations in two types of hairpins as shown by spectroscopic studies and molecular dynamic calculations. Structures of DNA oligonucleotides are closely related to their biological functions, such as the inhibition of telomerase and thrombin activity by DNA quadruplex structures. Detection of quadruplex formation has been well studied for quadruplexes associated via intramolecular folding or dimerization of hairpin structures. Our work reports studies on intermolecular quadruplex association via monitoring excimer fluorescence of pyrene probed G-rich sequences. In general, chair-type quadruplex structures show high affinity and inhibition to thrombin. Thrombin binding agents possessing modified loop regions have been designed and synthesized. A two-step unfolding mechanism has been proposed and investigated via different spectroscopic techniques.

Last modified

• 08/28/2018

Creator

• Hui he Zhu

DOI

• https://doi.org/10.21985/N2742T

Subject

• Chemistry

Keyword

• Chemistry
• Organic

Date created

• 2007-11-29

Resource type

• Dissertation

Rights statement

• In Copyright