The scope of this review is the nature and dynamics of the singlet excited electronic states created in nucleic acids and their constituents by UV light. Interest in the UV photochemistry of nucleic acids has long been the motivation for photophysical studies of the excited states, because these states are at the beginning of the complex chain of events that culminates in photodamage. UV-induced damage to DNA has profound biological consequences, including photocarcinogenesis, a growing human health problem.1-3 Sunlight, which is essential for life on earth, contains significant amounts of harmful UV (λ < 400 nm) radiation. These solar UV photons constitute one of the most ubiquitous and potent environmental carcinogens. This extraterrestrial threat is impressive for its long history; photodamage is as old as life itself. The genomic information encoded by these biopolymers has been under photochemical attack for billions of years. It is not surprising then that the excited states of the nucleic acid bases (see Chart 1), the most important UV chromophores of nucleic acids, are highly stable to photochemical decay, perhaps as a result of selection pressure during a long period of molecular evolution. This photostability is due to remarkably rapid decay pathways for electronic energy, which are only now coming into focus through femtosecond laser spectroscopy. The recently completed map of the human genome and the ever-expanding crystallographic database of nucleic acid structures are two examples that illustrate the richly detailed information currently available about the static properties of nucleic acids. In contrast, much less is known about the dynamics of these macromolecules. This is particularly true of the dynamics of the excited states that play a critical role in DNA photodamage. Efforts to study nucleic acids by time-resolved spectroscopy have been stymied by the apparent lack of suitable fluorophores. In contrast, dynamical spectroscopy of proteins has flourished thanks to intrinsically fluorescent amino acids such as tryptophan, tyrosine, and phenylalanine.4 The primary UVabsorbing constituents of nucleic acids, the nucleic acid bases, have vanishingly small fluorescence quantum yields under physiological conditions of temperature and pH.5 In fact, the bases were frequently described as “nonfluorescent” in the early literature. * To whom correspondence should be addressed. E-mail: kohler@ chemistry.ohio-state.edu. Phone: (614) 688-3944. Fax: (614) 2921685. 1977 Chem. Rev. 2004, 104, 1977−2019

Ultrafast Excited-State Dynamics in Nucleic Acids

To study the operational behaviour of λ-terms, we will use the denotational (mathematical) approach. A denotational semantics for a language is based on the choice of a space of semantics values, or denotations, where terms are to be interpreted. Choosing a space with nice mathematical properties can help in proving the semantic properties of terms, since to this aim standard mathematical techniques can be used.

λ Δ -Models

CRISPR-Cas systems that provide defence against mobile genetic elements in bacteria and archaea have evolved a variety of mechanisms to target and cleave RNA or DNA(1). The well-studied types I, II ...

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.

Automated exploration of the low-energy chemical space with fast quantum chemical methods

Solar ultraviolet light creates excited electronic states in DNA that can decay to mutagenic photoproducts. This vulnerability is compensated for in all organisms by enzymatic repair of photodamaged DNA. As repair is energetically costly, DNA is intrinsically photostable. Single bases eliminate electronic energy non-radiatively on a subpicosecond timescale1, but base stacking and base pairing mediate the decay of excess electronic energy in the double helix in poorly understood ways. In the past, considerable attention has been paid to excited base pairs2. Recent reports have suggested that light-triggered motion of a proton in one of the hydrogen bonds of an isolated base pair initiates non-radiative decay to the electronic ground state3,4. Here we show that vertical base stacking, and not base pairing, determines the fate of excited singlet electronic states in single- and double-stranded oligonucleotides composed of adenine (A) and thymine (T) bases. Intrastrand excimer states with lifetimes of 50–150 ps are formed in high yields whenever A is stacked with itself or with T. Excimers limit excitation energy to one strand at a time in the B-form double helix, enabling repair using the undamaged strand as a template.

Base stacking controls excited-state dynamics in A·T DNA

The vibronic spectrum of laser desorbed and jet cooled guanine consists of bands from three different tautomers of guanine as revealed by UV–UV and IR–UV double resonance spectroscopy. 1-methylguanine, in which the Keto–Enol tautomerism is blocked, shows hole burning spectra from the 9H-and 7H-Keto form. A comparison of the vibronic pattern of the different tautomers demonstrates that the vibronic spectrum built on the redmost guanine band at 32 870 cm−1 (electronic origin 0) can be traced back to the 9H-Enol tautomer, while the spectra built on the origins at 0+404 cm−1 and 0+1044 cm−1 stem from the two Keto tautomers. The IR–UV double resonance spectra of the OH-and NH-stretch vibrations of the different tautomers support this assignment. The UV and IR spectra can be partly assigned by comparison with ab initio calculated vibrational frequencies and with the help of deuteration experiments.

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Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy

We present R2PI, IR–UV and UV–UV double resonance measurements of the guanine–cytosine (G–C) dimer formed in a supersonic jet. We show that there is only one isomer of G–C in the investigated wavelength range from 33200 to 34100 cm−1. We assigned the observed G–C isomer to a specific structure, based on comparisons of the IR spectra of the G and C monomers with the G–C dimer in the range of the OH and NH stretching vibrations and ab initio-calculated vibrational frequencies and dimer stabilities. The cluster exhibits an HNH⋯O/NH⋯N/CO⋯HNH bonding similar to the Watson–Crick G–C base pair bonding but with C as the enol tautomer. We did not observe any keto–keto or enol–enol G–C dimers in the investigated wavelength region.

/pdf/pairing-of-the-nucleobases-guanine-and-cytosine-in-the-gas-4jgyitedvi.pdf

Pairing of the nucleobases guanine and cytosine in the gas phase studied by IR–UV double-resonance spectroscopy and ab initio calculations

In this paper we present detailed R2PI spectra with IR–UV and UV–UV double resonance measurements of the guanine dimer (GG) and its methylated derivatives. We show that there are two isomers of GG in the investigated wavelength range from 32565 to 33600 cm−1. We were able to assign the two isomers to specific structures based on comparison of the intermolecular vibronic patterns of the dimers with and without methylation, on analysis of the IR spectra in the range of the OH and NH stretching vibrations and on comparison with ab initio calculated dimer stabilities and vibrational frequencies. In both structures both guanine moieties are in the keto tautomeric form, even though the enol tautomers are also present in the beam. One isomer exhibits nonsymmetric hydrogen bonding with HNH⋯N, NH⋯N and CO⋯HNH interactions (K9K7-2). The other isomer has a symmetrical hydrogen bond arrangement with CO⋯NH/NH⋯OC
bonding (K9K7-1). The most stable guanine dimer forms CO⋯NH/NH⋯OC hydrogen bonds and has C2h symmetry (K9K9-1). Due to its strong exciton splitting the allowed S0–S2 transition is outside the investigated spectral range. We did not observe any keto–enol or enol–enol dimers in the investigated wavelength region. The calculations predict these dimers to be considerably less stable.

http://www.bgu.ac.il/~eyalnir/Materials/AA-Mine/Ph.D/11-Pairing%20of%20the%20nucleobase%20guanine%20studied%20by%20IR-UV%20double-resonance%20spectroscopy%20and%20ab%20initio%20calculations.pdf

Pairing of the nucleobase guanine studied by IR–UV double-resonance spectroscopy and ab initio calculations

To observe fundamental properties of DNA building blocks it is desirable to study individual nucleosides in the gas phase without interference from solvent molecules, or macromolecular structure. As a first step, we have recently reported the first vibronic spectrum of the nucleobase guanine, obtained by a combination of laser desorption, jet cooling, and resonance enhanced multiphoton ionization (REMPI).1 Although guanine is important as a chromophore in DNA, it is more realistic for understanding the photochemistry of DNA to study the nucleosides. Those are even harder to vaporize intact because they are thermally more labile and, with their larger molecular weights, have still lower vapor pressures. Using laser desorption, we have now succeeded in forming a molecular beam of nucleosides, and we report the first REMPI spectra of a series of individual guanosines, namely guanosine (Gs), 2′deoxyguanosine (2′deoxyGs), and 3′deoxyguanosine (3′deoxyGs). We compare our results with computations at the HF 6-31G(d,p) level. The results suggest the occurrence of two different conformations, each probably stabilized by internal hydrogen bonds. One of those two conformations is absent in 2′deoxyGs implying that the 2′ hydroxyl group is required for its stabilization. Spectroscopic properties of guanosines have been studied primarily by Raman techniques in solution.2-9 A great deal of attention has been given to potential Raman markers for hydrogen bonding and for structural conformation. Observation of hydrogen bonding by Raman spectroscopy requires identification of vibrations that depend strongly on those specific atoms in guanine, that serve as either proton donor or acceptor. However, most vibrations involve the concerted motion of multiple atoms, and therefore correlation of marker frequencies with specific hydrogen bonding sites is not straightforward. Guanosine vibrations involving motion along the glycosidic bond may provide conformational markers if their frequencies are sensitive to puckering of the ribose ring or for rotation around the sugar-base bond. Interpretation of these markers requires careful analysis of complex vibrational modes. On the other hand, different conformations can be observed much more directly by vibronic spectroscopy when they produce multiple origins. As we will show below, we observe two origins in our spectra, which we can associate with the syn and the anti orientations of the base relative to the ribose moiety. We have published details of our setup for laser desorption jet cooling REMPI spectrometry elsewhere.10 Sample preparation consisted of depositing neat material in powder form on graphite substrates. We moved the substrate slowly while acquiring spectra, gradually exposing fresh material. For desorption we used pulses from a Nd:YAG laser at 1064 nm with fluences on the order of 1 mJ/cm2. Desorbed neutral molecules were entrained in a supersonic expansion with Ar drive gas, injected by a pulsed solenoid valve. Downstream, the entrained molecules were onecolor two-photon photoionized, and the ions were detected in a reflectron time-of-flight mass spectrometer. The first photon resonantly excites the molecule, while a second photon from the same laser ionizes the excited molecule. By varying the wavelength while monitoring specific mass peaks we obtained mass selected excitation spectra. The typical ionization laser fluence was on the order of 0.1 mJ/cm2. Figure 1 shows the REMPI spectra of (a) Gs, (b) 3′deoxyGs, and (c) 2′deoxyGs. We assign the lowest-energy peak in each of the spectra as a 0-0 transition to the S1 excited state. Careful scans to lower energy by 1000 cm-1 do not reveal any additional peaks. The same was true when performing two-color ionization with a second photon at 193 nm. Therefore, we do not believe that we are observing a cutoff in the spectrum related to the ionization potential of Gs. Furthermore we have measured the ionization potential of guanine as 8.1 eV by two-color ionization.11,12 That is 1 eV less than the two-photon energy at the Gs origin. † Heinrich Heine Universität. (1) Nir, E.; Grace, L.; Brauer, B.; de Vries, M. S. J. Am. Chem. Soc. 1999, 121, 4896. (2) Faurskov-Nielsen, O.; Lund, P.; Petersen, S. J. Raman Spectrosc. 1981, 11, 493. (3) Nishimura, Y.; Tsuboi, M.; Sato, T.; Aoki, K. J. Mol. Struct. 1986, 146, 123. (4) Chinsky, L.; Jolles, B.; Laigle, A.; Turpin, P. J. Raman Spectrosc. 1987, 18, 195. (5) Carmona, P.; Molina, M. J. Mol. Struct. 1990, 219, 323. (6) Toyama, A.; Takino, Y.; Takeuchi, H.; Harada, I. J. Am. Chem. Soc. 1993, 115, 11092. (7) Urabe, H.; Sugawara, Y.; Kasuya, T. Phys. ReV. B 1995, 51, 5666. (8) Toyama, A.; Hamuara, M.; Takeuchi, H. J. Mol. Struct. 1996, 15, 99. (9) Toyama, A.; Hanada, N.; Ono, J.; Yoshimitsu, E.; Takeuchi, H. J. Raman Spectrosc. 1999, 30, 623. (10) Meijer, G.; de Vries, M. S.; Hunziker, H. E.; Wendt, H. R. Appl. Phys. B 1990, 51, 395. (11) Hopkins, J. B.; Powers, D. R.; Smalley, R. E. J. Phys. Chem. 1981, 85, 3739. (12) Nir, E.; Grace, L.; de Vries, M. S. To be published. Figure 1. REMPI spectra of (a) guanosine, (b) 3′deoxyGs, and (c) 2′deoxyGs. In this energy range guanine itself does not exhibit any vibronic activity since its lowest energy peak is at 238 cm-1 above the origin. The syn and anti labels indicate origins of two possible conformers, and the numbers indicate vibrational modes and their combinations and overtones, for example 122 indicates one quantum of mode 1 and two quanta of mode 2; f indicates fundamental vibration. 8091 J. Am. Chem. Soc. 2000, 122, 8091-8092

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REMPI Spectroscopy of Laser Desorbed Guanosines.

A density functional study of [VO(O2)2(Im)]- (1, Im = imidazole) is presented, calling special attention to effects of dynamics and solvation on the 51V chemical shift. According to Car−Parrinello molecular dynamics simulations, rotation of the Im ligand can be fast in the gas phase, but is more hindered in aqueous solution. In the latter, bonding between Im and V is reinforced, and dynamic averaging of GIAO-B3LYP magnetic shieldings affords a gas-to-liquid shift of ca. −100 ppm for δ(51V). A complete catalytic cycle has been characterized for olefin epoxidation mediated by 1, using H2O2 as oxidant. The rate-determining step is indicated to be initial oxygen atom transfer from 1 to the substrate via a spiro-like transition state. Substituent effects on this barrier are examined, and a significant decrease (by 2−6 kcal/mol) is revealed upon removal of the Im proton or upon complexation with a H-bond acceptor. Implications for the mechanism of the oxidative chemistry of vanadium-dependent haloperoxidases an...

Petra Imhof

Papers

Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy

Pairing of the nucleobases guanine and cytosine in the gas phase studied by IR–UV double-resonance spectroscopy and ab initio calculations

Pairing of the nucleobase guanine studied by IR–UV double-resonance spectroscopy and ab initio calculations

REMPI Spectroscopy of Laser Desorbed Guanosines.

Peroxovanadate imidazole complexes as catalysts for olefin epoxidation: density functional study of dynamics, 51V NMR chemical shifts, and mechanism.