Femtosecond broadband time-resolved fluorescence and transient absorption investigation on the excited states of model DNA oligomers containing adenine

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Femtosecond broadband time-resolved fluorescence and transient absorption investigation on the excited states of model DNA oligomers containing adenine


Author: Ho, Yat Fung
Title: Femtosecond broadband time-resolved fluorescence and transient absorption investigation on the excited states of model DNA oligomers containing adenine
Degree: Ph.D.
Year: 2014
Subject: DNA -- Analysis.
Quadruplex nucleic acids.
Hong Kong Polytechnic University -- Dissertations
Department: Dept. of Applied Biology and Chemical Technology
Pages: xxiii, 292 p. : ill. (some col.) ; 30 cm.
Language: English
InnoPac Record: http://library.polyu.edu.hk/record=b2747252
URI: http://theses.lib.polyu.edu.hk/handle/200/7471
Abstract: Ultraviolet (UV) radiation on DNA produces electronically excited states that may cause damage to DNA. In contrast to the isolated DNA nucleic bases which have ultra-short excited state lifetimes (<~1 picosecond) for their remarkable photostability, the excited states of DNA in most cases exhibit much longer lifetime from several picoseconds to several nanoseconds. As a consequence, knowledge on the collective behavior of nucleic bases in DNA and its effect on the excited state dynamics are of pivotal importance for understanding the DNA photostability and the mechanism of DNA against the photodamage. Despite the large number of studies in the literature, the roles of base stacking and base pairing in the excited states of DNA remain an issue of intense debate. While femtosecond spectroscopic study using transient absorption suggested that stacking controls the excited state dynamics of double-stranded DNA, work conducted using femtosecond and nanosecond time-resolved emission indicated that the DNA excited states are complex, governed by an ensemble of factors relevant to the conformation of DNA. In addition, the electronic nature and dynamics of excitation transfer as well as how these are affected by factors such as the identity and sequence of the base content in DNA are also open questions in the photophysics and photochemistry of DNA. To help address these issues, we have performed femtosecond time-resolved spectroscopic investigation on a series of model DNA oligomers and the corresponding monomeric bases for comparison. A combined method of femtosecond broadband time-resolved fluorescence (fs-TRF), fluorescence anisotropy (fs-TRFA) and transient absorption (fs-TA) was employed to explore excited states and dynamics for single-stranded oligomers composed of adenine d(A)20 and thymine d(T)20 and double-stranded A/T DNAs in the form of d(A)20·d(T)20 and d(AT)10. We also conducted fs-TRF and fs-TRFA study on A and guanine (G) containing DNAs with varied length and different sequence as well as on a dimeric system nicotinamide adenine dinucleotide (NADH) and its related monomeric model compound 1-benzyl-1,4-dihydronicotinamide. By monitoring directly temporal evolution of the excited state spectra and at the same time the recovery of ground state bleach, the results we obtained for A/T DNAs provide solid evidence showing that the inter-base stacking is crucial in promoting excitation energy transfer and formation of long-lived excited state with lifetime of ~140 ps in d(A)20 and ~100 ps in d(A)20·d(T)20; the pairing interaction on the other hand plays a remarkable role in constraining the yield of long-lived excitation, reducing its contribution to the overall excited state decay from ~57% in the single-stranded d(A)20 to ~32% in the double-stranded d(A)20·d(T)20. Moreover, comparison of the fs-TRF and fs-TRFA data on the various A/G oligomers shows that the long-lived states (~200 ps lifetime) in these DNAs feature a largely common character arising due to charge transfer between G and adjacent A base but with the formation pathway depending on sequence of the A and G units. Finally, our results on NADH and its model compound present clear evidence for stacking controlled excitation energy transfer from A to nicotinamide which was found to proceed in ultrafast timescale (<100 fs) through a mechanism of exciton migration. The findings of our study suggest that bases stacking and bases pairing which are affected differently by the base components in DNA duplex both play a significant role in DNA excited state and in maintaining the photo-stability of genetic information in organism.

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