Structures and energetics of guanine tetrads and quadruplexes isolated in the gas phase

Azargun, Mohammad (2017) Structures and energetics of guanine tetrads and quadruplexes isolated in the gas phase. Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Structures, thermochemistries, reactivities, and kinetics of chemical systems in the gas phase can be determined by a variety of ion activation techniques. The internal energy of ions can be increased by colliding the accelerated ions with a target gas, collision-induced dissociation (CID). This technique can lead to a full or partial structural identification, and also to the relative stabilities of the ion clusters. Ions in the gas phase may reach a dissociation threshold by absorbing multiple photons from the laser radiation if the laser frequency is resonant with a vibrational mode which is called infrared multiphoton dissociation (IRMPD). This technique turns into IRMPD spectroscopy by varying the laser frequency and recording the resultant fragments as a function of laser frequency. Blackbody infrared radiative dissociation (BIRD) is another photodissociation technique used in this work that is well suited to slowly activate weakly-bound non-covalent interactions in order to determine their thermochemistries and also gain kinetic insights. Theoretical techniques have been used along with these activation techniques as a powerful complementary tool. This work provides physical chemistry insights about guanine tetrads and quadruplexes in the gas phase. The first phase of this research focuses on the alkali metal G-tetrads, M(9-eG)₄⁺ (M=Li, Na, K, Rb, Cs; 9eG = 9-ethylguanine). After their gas phase formation, their structures, stabilities, and energetics were examined by a combination of SORI-CID, IRMPD spectroscopy, and computational chemistry. The role of hydrogen bonding, the size of cation, and electrostatic interactions in the stability and structures were also examined. The formation of alkali metal G-quadruplexes, (M(9eG)₈⁺ (M = Na, K, Rb, Cs), was pursued in the next phase. The BIRD technique, in conjunction with master equation modeling, was applied to determine the binding energies and transition state nature of these G-quadruplexes. IRMPD spectroscopy, along with theoretical techniques, was used for structural elucidation. In the final step, gas phase formation of larger G-quadruplexes was assessed. The K₂(9-ethylguanine)₁₂⁺ quadruplex was successfully generated and isolated in the gas phase. BIRD and SORI-CID techniques were used to determine the quadruplex binding energies and gas phase stability, respectively. The structure of this quadruplex was determined by IRMPD spectroscopy and computational chemistry.

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