Deuterium Isotope Effect on Excited-State Dynamics in an Alternating GC Oligonucleotide

Abstract

Understanding how base pairing and stacking mediate the dissipation of electronic energy in DNA is essential for understanding the initial steps in UV photodamage. Excited states of individual DNA bases decay in solution to the ground state either directly by ultrafast internal conversion or, in the case of pyrimidine bases, indirectly via longer-lived triplet and 1 nπ*states. 1 The base stacking present in single-and double-stranded DNA causes these systems to have dramatically longer excited-state lifetimes compared to monomeric bases. [2][3][4][5] Femtosecond transient absorption experiments have detected long-lived excited states in numerous π-stacked systems from dinucleosides 5 to G-quadruplexes. 1 These long-lived states are formed in high yields only when π-stacking is present and are observed in stacks comprised of both AT and GC base pairs. 3,4,6 A recent model assigns these states to charge-transfer (CT) excited states or exciplexes formed between π-stacked bases that arise from initially populated Frenkel exciton states. [3][4][5] Although base stacking is clearly a requirement for the formation of these long-lived states, the consequences of base pairing on DNA excited-state dynamics is still highly uncertain and is the motivation for this study.The possibility that UV mutagenicity is a consequence of proton transfer between paired bases was proposed many years ago. 7 More recently, proton transfer was suggested to be responsible for the photostability of DNA. [8][9][10] Using IR-UV hole-burning spectroscopy, Abo-Riziq et al. observed a broad UV spectrum for isolated Watson Crick (WC) GC base pairs in the gas phase, whereas sharp UV spectra were observed for non-WC GC base pairing combinations. 11 The broad UV spectrum unique to GC base pairs in the WC conformation was suggested to result from lifetime shortening due to a proton transfer mechanism. Subsequent ab initio calculations implicated an ultrafast deactivation pathway between the excited 1 ππ* state and ground state mediated by proton transfer. 9,12 Recently, Schwalb and Temps reported shortened fluorescence lifetimes in isolated WC GC base pair analogs relative to the monomers in chloroform using fluorescence up-conversion spectroscopy. 13 However, because these model systems lack π-stacking interactions, their relevance to duplex DNA is uncertain.Here, we investigate the effect of base pairing on excited-state dynamics in GC-containing duplexes when base stacking is also present. This study is timely given recent reports of interand intrastrand charge transfer states in computational studies of excited states in doublestranded DNA. 9,12,[14][15][16] We report the discovery of a pronounced isotope effect on excited- Figure 1. Figure 1 shows that there is significantly faster ground-state recovery for d(GC) 9 ·d(GC) 9 in H 2 O compared to D 2 O. In contrast, only a minor isotope effect (Figure 1 inset) is observed on the more rapidly decaying signals for an equimolar mixture of the 5′-mononucleotides, CMP and GMP. Circular dichroism spectr...

Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism

“…The SDHT decay will compete with the monomeric non-radiative photochemical channel. Also with intrastrand phenomena such as the formation of exciplexes between π-stacked NABs, as suggested by experiments in alternating and non-alternating GC oligonucleotides 89,91 and previous computations on related systems. 52,63,118 The efficiency of the hydrogen/proton energy-decay pathways in DNA will depend on the degree of hydrogen-bonding between the strands.…”

“…The long-lived exciplexes, as a consequence of π-stacking, are however sensitive to deuterium substitution at the hydrogen bonds, showing therefore that proton/hydrogen transfers are still present. 90,91 Qualitative predictions for these processes can be established from our calculations. At the time of UV irradiation of the GC base pair, those molecules with a certain momentum in the N' 3 …H 1 N 1 direction (for instance, Sim2 and Sim4) might undergo a double hydrogen-transfer process, resulting in the production of the TAU1 configuration or restoring the WC structure.…”

“…89,91 In general, new photochemical routes are accessible in the UV-irradiated GC base pair, which will compete with the energy-decay pathways of the isolated NABs and π-stacked (or intrastrand) dimers.…”

“…96 The authors of this work have also suggested that the photoinduced hydrogen transfer cannot be considered as a relevant deactivation path in DNA. However, the most recent experiments from de La Harpe et al have reported pronounced isotope effects on the long-lived exciplex excited states of a d(GC) 9 ·d(GC) 9 double-strand, 91 in agreement with independent studies by Doorley et al 90 In this scenario, a model based on the fully characterization of the energy-decay channels involving proton/hydrogen transfer in the GC base pair seems timely in order to establish the operative mechanisms for photostability and tautomerism and to shed some light into the relevance of basepairing in the photodynamics of DNA. Especially important shall be certain aspects related to the photochemical channels connecting the WC base pair with other tautomeric configurations.…”

Photoreaction channels of the guanine–cytosine base pair explored by long-range corrected TDDFT calculations

“…[11][12][13][14][15] In spectroscopic experiments, the effect of hydrogen bonding on the excited-state lifetime of the base pairs has been of great interest. [16][17][18][19][20][21][22][23][24][25][26] In the present work, excited-state potential energy profiles of the Watson-Crick form of the guaninecytosine (GC) base pair are theoretically studied for all of the potentially competing reactions mentioned above: SPT and DPT between guanine (G) and cytosine (C) as well as nonradiative decay in each single base under hydrogen bonding. One purpose of this study is to assess the favorability of the decay process in the G monomer with hydrogen-bonded to C, which was rarely discussed in previous studies.…”