Karl Kleinermanns

Pairing of isolated nucleic-acid bases in the absence of the DNA backbone

The two intertwined strands of DNA are held together through base pairing—the formation of hydrogen bonds between bases located opposite each other on the two strands. DNA replication and transcription involve the breaking and re-forming of these hydrogen bonds, but it is difficult to probe these processes directly. For example, conventional DNA spectroscopy is dominated by solvent interactions, crystal modes and collective modes of the DNA backbone; gas-phase studies, in contrast, can in principle measure interactions between individual molecules in the absence of external effects, but require the vaporization of the interacting species without thermal degradation. Here we report the generation of gas-phase complexes comprising paired bases, and the spectroscopic characterization of the hydrogen bonding in isolated guanine–cytosine (G–C) and guanine–guanine (G–G) base pairs. We find that the gas-phase G–C base pair adopts a single configuration, which may be Watson–Crick, whereas G–G exists in two different configurations, and we see evidence for proton transfer in the G–C pair, an important step in radiation-induced DNA damage pathways. Interactions between different bases and between bases and water molecules can also be characterized by our approach, providing stringent tests for high-level ab initio computations that aim to elucidate the fundamental aspects of nucleotide interactions.

High resolution UV spectroscopy of phenol and the hydrogen bonded phenol‐water cluster

The S1←S0 000 transitions of phenol and the hydrogen bonded phenol(H2O)1 cluster have been studied by high resolution fluorescence excitation spectroscopy. All lines in the monomer spectrum are split by 56±4 MHz due to the internal rotation of the −OH group about the a axis. The barrier for this internal motion is determined in the ground and excited states; V2″=1215 cm−1, and V2′=4710 cm−1. The rotational constants for the monomer in the ground state are in agreement with those reported in microwave studies. The excited state rotational constants were found to be A′=5313.7 MHz, B′=2620.5 MHz, and C′=1756.08 MHz. The region of the redshifted 000 transition of phenol(H2O)1 shows two distinct bands which are 0.85 cm−1 apart. Their splitting arises from a torsional motion which interchanges the two equivalent H atoms in the H2O moiety of the cluster. This assignment was confirmed by spin statistical considerations. Both bands could be fit to rigid rotor Hamiltonians. Due to the interaction between the overal...

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

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.

Excited state dynamics of DNA bases

Biochemical reactions are subject to the particular environmental conditions of planet earth, including solar irradiation. How DNA responds to radiation is relevant to human health because radiation damage can affect genetic propagation and lead to cancer and is also important for our understanding of how life on earth developed. A reductionist approach to unravelling the detailed photochemistry seeks to establish intrinsic properties of individual DNA building blocks, followed by extrapolation to larger systems, to incorporate interactions between the building blocks and the role of the biomolecular environment. Advances in both experimental and computational techniques have lead to increasingly detailed insights in the excited state dynamics of DNA bases in isolation as well as the role of the solvent and intermolecular interactions. This review seeks to summarise current findings and understanding.

Tautomers and electronic states of jet-cooled adenine investigated by double resonance spectroscopy

We present resonant two-photon ionization (R2PI) and IR-UV double resonance spectra of the nucleobase adenine seeded in a supersonic jet. We show that there are two tautomers of adenine which absorb in the wavelength range 35 400 to 36 700 cm−1. The IR spectra, measured in the range 3200 to 3700 cm−1via hole burning at 36 105 (35 824) cm−1, show bands at 3452 (3437), 3508 (3507/3514) and 3569 (3550) cm−1, which we assign to the symmetric NH2, N–H and antisymmetric NH2 stretching vibrations of the 9H-(7H-) tautomers of adenine by comparison with ab initio based normal mode calculations. The IR spectrum taken via a much weaker band at 35 497 cm−1 agrees completely with the 9H spectrum analysed at 36 105 cm−1 so that an earlier hypothesis (N. J. Kim, G. Jeong, Y. S. Kim, J. Sung and S. K. Kim, J. Chem. Phys., 2000, 113, 10 051, ) of an nπ* transition contributing to the red part of the spectrum is very probable. It is shown that the conventional IR absorption spectrum of adenine in the gas phase is a superposition of the IR spectra of the 9H- and 7H-tautomers and possibly other tautomers. Despite the short lifetime of electronically excited adenine we were able to perform two-color R2PI to obtain the ionization threshold of the 9H tautomer (69 400 ± 50 cm−1 = 8.606 ± 0.006 eV).

Structure and vibrations of phenol(H2O)7,8 studied by infrared-ultraviolet and ultraviolet-ultraviolet double-resonance spectroscopy and ab initio theory

The vibronic spectra of jet cooled phenol(H2O)7,8 clusters were analyzed with mass selective resonance enhanced two photon ionization (R2PI) and ultraviolet-ultraviolet spectral hole burning (UV-UV SHB). A double resonance technique with an infrared (IR) laser as burn laser (IR-UV SHB) was used to measure the intramolecular OH stretching vibrations of the mass- and isomer-selected clusters. Two isomers of phenol(H2O)7 and three isomers of phenol(H2O)8 could be distinguished via SHB and their IR spectra recorded. The red- or blueshift of the electronic origin relative to the phenol monomer gives valuable hints on the hydrogen bonding between phenol and the water moiety. All IR spectra contain four characteristic groups of OH stretching vibrations which give insight into the structure of the H bonded network. The ab initio calculations show that the minimum energy structures for phenol(H2O)7,8 are very similar to the corresponding water clusters which are based on regular (H2O)8 cubes. Comparison between ex...

Conformers of the peptides glycine-tryptophan, tryptophan-glycine and tryptophan-glycine-glycine as revealed by double resonance laser spectroscopy

The peptides Trp-Gly, Gly-Trp and Trp-Gly-Gly were investigated by UV–UV and IR–UV hole burning spectroscopy. Solid samples of the three peptides were vaporised into an argon jet by laser desorption. The IR–UV spectra of different conformers of the peptides were assigned by comparison with the IR–UV spectra of tryptophan [Snoek et al., Phys. Chem. Chem. Phys., 2001, 3, 1819], the free peptide bond in N-acetyl tryptophan methyl amide [Dian et al., J. Chem. Phys., 2002, 117, 10688] and ab initio calculations performed at the DFT B3LYP 6-31G(d,p) level. Apart from an NH⋯NH2 interaction, the peptide backbone of one conformer of each dipeptide is unfolded. The second conformer of Gly-Trp shows a COOH⋯OC hydrogen bond and the second conformer of Trp-Gly-Gly a hydrogen bond between the peptide backbone and the NH group of the indole ring.

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

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.

Structure and vibrations of phenol(H2O)2

Extensive ab initio calculations at the Hartree–Fock (HF) level using different basis sets have been performed in order to obtain the minimum energy structure of the phenol(H2O)2‐cluster. Several hydrogen bonding arrangements and a van der Waals structure are discussed. The most stable structure turns out to be cyclic with nonlinear hydrogen bonds. This structure is similar to the one calculated for the water trimer. In contrast with the water trimer the average binding energy of a hydrogen bond decreases with increasing cluster size of Ph(H2O)n (n=1,2). This is a result of non equal hydrogen bonds. A normal coordinate analysis has been carried out for the fully optimized minimum energy structure of phenol(H2O)2 and its deuterated isotopomer d‐phenol(D2O)2. The calculated harmonic intramolecular vibrational modes are compared with experimental values and the intermolecular stretching vibrations are assigned.

IR-UV double-resonance spectroscopy of the nucleobase adenine

We present R2PI and IR–UV double resonance spectra of the nucleobase adenine seeded in a supersonic jet. We show that there is only one tautomer of adenine which absorbs in the wavelength range 36 050 to 36 700 cm−1. The IR spectra, measured in the range 3200 to 3700 cm−1, show bands at 3452, 3508 and 3569 cm−1, which we assign to the symmetric NH2 , N–H and antisymmetric NH2 stretching vibrations of a single tautomer of adenine. We compare the experimental IR–UV double resonance spectra with ab initio based normal mode calculations. The observed tautomer is most probably the 9H amino-form of adenine.