A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol
Abstract not provided
Aller, Pierre↗
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Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction
A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye–dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
The Radiation Stability of Thymine in Solid H2O
Nucleobases are of significant importance to all known organisms, may be an important building block of life, and could be important biosignatures of current or past life. Given their potential significance to the field of astrobiology, it is important to understand the survival of these molecules when subjected to ionizing radiation as is present in a range of extraterrestrial environments. In this work we present data on the kinetics of the radiolytic destruction of pure thymine, and water + thymine ice mixtures at temperatures from 13 to 150 K. Rate constants were measured using in situ infrared spectroscopy and radiolytic half-lives for thymine were computed for different planetary and interstellar environments. Our results demonstrate that the survival of thymine decreases as the dilution of thymine in water increases. Additionally, we find that thymine survival increases with ice temperature and that this decrease may be related to structure of the ice matrix.
nucleobases, radiolysis, astrobiology↗
Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers
Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining considerable interest. New methods to improve the rigidity of the DNA scaffold and thus the stability of the molecular dye aggregates to encourage exciton delocalization are desired. In these dye–DNA constructs, one potential way to increase the stability of the aggregates is to create an additional covalent bond via photo-cross-linking reactions between thymines in the DNA scaffold. Specifically, we report an approach to increase the yield of photo-cross-linking reaction between thymines in the core of a DNA Holliday junction while limiting the damage from UV irradiation to DNA. We investigated the effect of the distance between thymines on the photo-cross-linking reaction yields by using linkers with different lengths to tether the dyes to the DNA templates. By comprehensively evaluating the photo-cross-linking reaction yields of dye–DNA aggregates using linkers with different lengths, we conclude that interstrand thymines tend to photo-cross-link more efficiently with short linkers. A higher cross-linking yield was achieved due to the shorter intermolecular distance between thymines influenced by strong dye–dye interactions. Furthermore, our method establishes the possibility of improving the stability of DNA-scaffolded dye aggregates, thereby expanding their use in exciton-based applications such as light harvesting, nanoscale computing, quantum computing, and optoelectronics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electron accommodation dynamics in the DNA base thymine
The dynamics of electron attachment to the DNA base thymine are investigated using femtosecond time-resolved photoelectron imaging of the gas phase iodide-thymine (I{sup −}T) complex. An ultraviolet pump pulse ejects an electron from the iodide and prepares an iodine-thymine temporary negative ion that is photodetached with a near-IR probe pulse. The resulting photoelectrons are analyzed with velocity-map imaging. At excitation energies ranging from −120 meV to +90 meV with respect to the vertical detachment energy (VDE) of 4.05 eV for I{sup −}T, both the dipole-bound and valence-bound negative ions of thymine are observed. A slightly longer rise time for the valence-bound state than the dipole-bound state suggests that some of the dipole-bound anions convert to valence-bound species. No evidence is seen for a dipole-bound anion of thymine at higher excitation energies, in the range of 0.6 eV above the I{sup −}T VDE, which suggests that if the dipole-bound anion acts as a “doorway” to the valence-bound anion, it only does so at excitation energies near the VDE of the complex.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Transient resonant Auger–Meitner spectra of photoexcited thymine
In this paper, we present the first investigation of excited state dynamics by resonant Auger–Meitner spectroscopy (also known as resonant Auger spectroscopy) using the nucleobase thymine as an example. Thymine is photoexcited in the UV and probed with X-ray photon energies at and below the oxygen K-edge. After initial photoexcitation to a ππ* excited state, thymine is known to undergo internal conversion to an nπ* excited state with a strong resonance at the oxygen K-edge, red-shifted from the ground state π* resonances of thymine. We resolve and compare the Auger–Meitner electron spectra associated both with the excited state and ground state resonances, and distinguish participator and spectator decay contributions. Furthermore, we observe simultaneously with the decay of the nπ* state signatures the appearance of additional resonant Auger–Meitner contributions at photon energies between the nπ* state and the ground state resonances. We assign these contributions to population transfer from the nπ* state to a ππ* triplet state via intersystem crossing on the picosecond timescale based on simulations of the X-ray absorption spectra in the vibrationally hot triplet state. Moreover, we identify signatures from the initially excited ππ* singlet state which we have not observed in our previous study.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mechanisms for the formation of thymine under astrophysical conditions and implications for the origin of life
Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H{sub 2}O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H{sub 2}O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H{sub 2}O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mechanisms for the Formations of the Thymine Under Astrophysical Conditions and Implications for the Origin of Life
Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.
Origin↗
Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases
Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
59 BASIC BIOLOGICAL SCIENCES↗
Observation of Ultrafast Intersystem Crossing in Thymine by Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy
We studied the photoinduced ultrafast relaxation dynamics of the nucleobase thymine using gas-phase time-resolved photoelectron spectroscopy. Employing extreme ultraviolet pulses from high harmonic generation for photoionization, we substantially extend our spectral observation window with respect to previous studies. This enables us to follow relaxation of the excited state population all the way to low-lying electronic states including the ground state. In thymine, we observe relaxation from the optically bright $^1ππ*$ state of thymine to a dark $^1nπ*$ state within 80 ± 30 fs. The $^1nπ*$ state relaxes further within 3.5 ± 0.3 ps to a low-lying electronic state. By comparison with quantum chemical simulations, we can unambiguously assign its spectroscopic signature to the $^3ππ*$ state. Hence, our study draws a comprehensive picture of the relaxation mechanism of thymine including ultrafast intersystem crossing to the triplet manifold.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Photoinduced hydrogen dissociation in thymine predicted by coupled cluster theory
The fate of thymine upon excitation by ultraviolet radiation has been the subject of intense debate. Today, it is widely believed that its ultrafast excited state gas phase decay stems from a radiationless transition from the bright ππ* state to a dark nπ* state. However, conflicting theoretical predictions have made the experimental data difficult to interpret. Here we simulate the early gas phase ultrafast dynamics in thymine at the highest level of theory to date. This is made possible by performing wavepacket dynamics with a recently developed coupled cluster method. Our simulation confirms an ultrafast ππ* to nπ* transition (τ = 41 ± 14 fs). Furthermore, the predicted oxygen-edge X-ray absorption spectra agree quantitatively with experiment. We also predict an as-yet uncharacterized πσ* channel that leads to hydrogen dissociation at one of the two N-H bonds. Similar behavior has been identified in other heteroaromatic compounds, including adenine, and several authors have speculated that a similar pathway may exist in thymine. However, this was never confirmed theoretically or experimentally. This prediction calls for renewed efforts to experimentally identify or exclude the presence of this channel.
Kjønstad, Eirik F.↗
Modified Iterative Extended Hueckel. 2: Application to the interaction of Na(+), Na(+)(aq.), Mg(+)-2(aq.) with adenine and thymine
Modified Iterative Extended Hueckel, which includes explicit effective internuclear and electronic interactions, is applied to the study of the energetics of Na(+),Mg(+), Na(+) (aqueous), and Mg(+2) (aqueous) ions approaching various possible binding sites on adenine and thymine. Results for the adenine + ion and thymine + ion are in good qualitative agreement with ab initio work on analogous systems. Energy differences between competing sites are in excellent agreement. Hydration appears to be a critical factor in determining favorable binding sites. That the adenine Nl and N3 sites cannot displace a water molecule from the hydrated cation indicates that they are not favorable binding sites in aqueous media. Of those sites investigated, 04 was the most favorable binding site on the thymine for the bare Na(+). However, the 02 site was the most favorable binding site for either hydrated cation.
Aronowitz, S.↗
Temperature dependence of the cross section for the fragmentation of thymine via dissociative electron attachment
Providing experimental values for absolute Dissociative Electron Attachment (DEA) cross sections for nucleobases at realistic biological conditions is a considerable challenge. In this work, we provide the temperature dependence of the cross section, σ, of the dehydrogenated thymine anion (T − H){sup −} produced via DEA. Within the 393-443 K temperature range, it is observed that σ varies by one order of magnitude. By extrapolating to a temperature of 313 K, the relative DEA cross section for the production of the dehydrogenated thymine anion at an incident energy of 1 eV decreases by 2 orders of magnitude and the absolute value reaches approximately 6 × 10{sup −19} cm{sup 2}. These quantitative measurements provide a benchmark for theoretical prediction and also a contribution to a more accurate description of the effects of ionizing radiation on molecular medium.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy
In this work, the relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74–5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ~400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ~600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multistate hybrid time-dependent density functional theory with surface hopping accurately captures ultrafast thymine photodeactivation
We report an efficient analytical implementation of first-order nonadiabatic derivative couplings between arbitrary Born–Oppenheimer states in the hybrid time-dependent density functional theory (TDDFT) framework using atom-centered basis functions. Our scheme is based on quadratic response theory and includes orbital relaxation terms neglected in previous approaches. Simultaneous computation of multiple derivative couplings and energy gradients enables efficient multistate nonadiabatic molecular dynamics simulations in conjunction with Tully's fewest switches surface hopping (SH) method. We benchmark the thus obtained multistate TDDFT-SH scheme by simulating ultrafast decay of UV-photoexcited thymine, for which accurate gas-phase data from ultrafast spectroscopy experiments are available. The calculations predict a fast 153 fs decay from the bright S 2 to the dark S 1 excited state, followed by a much slower 14 ps S 1 deactivation to the ground state; statistical uncertainties were estimated using bootstrap sampling. These results agree well with the experimentally observed time constants of 100–200 fs and 5–7 ps, respectively, unlike previous multiconfigurational self-consistent field and second-order algebraic diagrammatic construction calculations. Furthermore, our results support the S 1 -trapping hypothesis. For thymine, the computational cost of a single TDDFT-SH time-step including the lowest 3 states, all couplings and gradients, is ~5 times larger than the cost of a single Born–Oppenheimer dynamics time step for the ground state in our implementation. Thus, ps nonadiabatic dynamics simulations using multistate hybrid TDDFT-SH for systems with up to ~100 atoms are possible without drastic approximations on single workstation nodes. Our implementation will be made available through Turbomole.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystallographic evidence of Watson–Crick connectivity in the base pair of anionic adenine with thymine
Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N 4444 ] + ) or tetrabutylphosphonium ([P 4444 ] + ) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N 4444 ][Ad]·2H 2 O, and thymine, [P 4444 ][Thy]·2H 2 O, as well as the double salt cocrystal, [P 4444 ] 2 [Ad][Thy]·3H 2 O·2HThy. The cocrystal includes the anionic [Ad-(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson–Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.
59 BASIC BIOLOGICAL SCIENCES↗
Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA
Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G·T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5- carboxylcytosine (caC), which are generated from mC by Tet (ten–eleven translocation) enzymes. Using improved crystallization conditions, we solved high resolution (up to 1.45 A) structures of TDG enzyme– ' product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water mediated enzyme–substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNAfree TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme–product complex.
59 BASIC BIOLOGICAL SCIENCES↗
Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues
Thymine DNA Glycosylase (TDG) is a base excision repair enzyme functioning in DNA repair and epigenetic regulation. TDG removes thymine from mutagenic G·T mispairs arising from deamination of 5-methylcytosine (mC), and it processes other deamination-derived lesions including uracil (U). Essential for DNA demethylation, TDG excises 5- formylcytosine and 5-carboxylcytosine, derivatives of mC generated by Tet (ten-eleven translocation) enzymes. Here, we report structural and functional studies of TDG82-308, a new construct containing 29 more N-terminal residues than TDG111-308, the construct used for previous structures of DNAbound TDG. Crystal structures and NMR experiments demonstrate that most of these N-terminal residues are disordered, for substrate- or productbound TDG82-308. Nevertheless, G·T substrate affinity and glycosylase activity of TDG82-308 greatly exceeds that of TDG111-308 and is equivalent to full-length TDG. We report the first high-resolution structures of TDG in an enzyme-substrate complex, for G·U bound to TDG82-308 (1.54 A) and TDG ' 111-308 (1.71 A), revealing ' new enzyme-substrate contacts, direct and watermediated. We also report a structure of the TDG82-308 product complex (1.70 A). TDG ' 82-308 forms unique enzyme–DNA interactions, supporting its value for structure-function studies. The results advance understanding of how TDG recognizes and removes modified bases from DNA, particularly those resulting from deamination.
59 BASIC BIOLOGICAL SCIENCES↗