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Pair Formation of Free Nucleobases and Mononucleosides in the Gas Phase

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Pair Formation of Free Nucleobases and Mononucleosides in the Gas Phase Pair Formation of Free Nucleobases and Mononucleosides in the Gas Phase Michael Dey, Jürgen Grotemeyer1 Institut für Physikalische Chemie, Universität Würzburg, Marcusstr. 9/10, 97070 Würzburg, Germany Edward W. Schlag Institut für Physikalische Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany Z. Naturforsch. 49a, 776-784 (1994); received May 20, 1994 The formation of neutral bimolecular clusters of unsubstituted nucleobases and mononucleosides in the gas phase has been studied by IR laser desorption of the neutral molecules into a supersonic beam expansion. The complementary nucleobase pairs adenine-thymine and cytosine-guanine of DNA have been found to be formed in preference to non complementary base pairs. Association constants for the formation of the dimers of free nucleobases and nucleosides in the gas phase are calculated from the experimental results. A strong influence due to side groups affecting the dimer formation of the nucleobases is shown. Introduction The complementary nucleobase pairing within the double helical structure of the DNA requires pairing The famous Watson-Crick structure of the double of each adenine residue with a thymine residue and stranded helix of nuclein acids [1] now celebrates its each cytosine residue with a guanine residue. Discus­ 40th anniversary. The forces causing the double sions about the formation of nucleobase pairs and the stranded structure of DNA are; hydrogen bonding be­ forces stabilizing them date back to the original dis­ tween complementary nucleobases of the two strands, covery of the DNA structure. Theoretical approaches hydrophobic forces formed by overlapping ^-systems to structures and stabilizing energies of nucleobase of the nucleobases of the two strands, steric forces due pairs were made in several theoretical attempts to to the rigid backbones - the sugar-phosphate chains predict gas phase [2, 3, 4, 5, 6] as well as liquid phase and interactions between phosphate ions of the DNA [7, 8, 9] behavior. Due to the number of atoms of and solvent molecules. The specific formation of nucleobase dimers however, simplifications of the cal­ adenine (A) and thymine (T) pairs on the one hand and culations are required such as using minimal base sets, cytosine (C) and guanine (G) on the other, the base reduction of geometric influences, estimation of some pairs exclusively occurring in DNA, may be a result of input values or the use of empirical or semi empirical these forces or of specific affinities of the nucleobases potentials. These simplifications, however, reduced themselves. the accuracy of most of the theoretical results for nu­ Our intention was to study unmodified nucleobases cleobase pair formation. and the corresponding mononucleosides in the gas Geometric complementary of the nucleobases in the phase in order to investigate whether the complemen­ double helical structure of the DNA was generally tary nucleobase pairs have native affinities or are me­ supposed to be the reason for the exclusive formation diated by external effects. It turned out that it is im­ of the Watson-Crick base pairs A-T and C-G. Investi­ portant to study the nucleobase pair formation in gation of isolated nucleobases and their interactions, absence of any side groups, which can be seen to lead however, is of interest to prove this statement. Some to false conclusions. nucleobase pair structures found in different environ­ ments are shown in Figure 1. Besides the hydrogen bonded Watson-Crick pairs (Fig. 1. 1 and 2) other Reprint requests to Prof. Dr. J. Grotemeyer, Institut für Physikalische Chemie, Universität Würzburg, Marcusstraße hydrogen bonded arrangements of free nucleobases 9/11, D-97070 Würzburg. have been found. These are due to hydrogen bonds 0932-0784 / 94 / 0700-0776 $ 06.00 © - Verlag der Zeitschrift für Naturforschung, D-72027 Tübingen M. Dey et al. • Pair Formation of Free Nueleobases in the Gas Phase 777 formed at other positions of the nueleobases. Cocrys­ the cluster behavior of the nueleobases. This change tallization of adenine and thymine may result in for­ will be referred to side group effects affecting the dimer mation of A-T pairs in the Hoogsten geometry [10] formation of nucleosides. (Figure 1. 3). However, not only hydrogen bonds may stabilize isolated nucleobase clusters, but also van der Experimental Waals interactions. Overlapping of the 7t-systems of nueleobases causes the formation of stacks of planar Experiments were performed with a reflection time parallel nueleobases (Figure 1. 4). The van der Waals of flight mass spectrometer (RETOF-MS) described in interactions, however, have only a limited speciflty, so detail in [25]. Therefore only a brief description is that a main formation of complementary base pairs presented here. A pulsed C 0 2 laser (Pulse System Inc.) due to these forces could not be observed. Stacked was used for desorption of the sample molecules. The base pairs are highly stabilized in aqueous solutions IR laser beam was slightly focused onto the solid sam­ due to hydrophobic forces between the nueleobases ple through a 8 cm ZnSe lens. A typical desorption [11]. The degree of formation of stacked base pairs in radiation used was 104 W/cm2 at 10.6 fim. The sample water, however, is mostly not due to interactions be­ probe was positioned ca. 1 mm in front of a pulsed jet tween the nueleobases but due to the influence of wa­ valve inside the desorption chamber. During a laser ter molecules [12, 13]. shot the pulsed valve was opened to emit a pulse of Ar Several experimental investigations of substituted atoms. The sample molecules were desorbed into a nucleobase pairs in the gas phase [14] and in different supersonic beam of Ar. The jet provides cooling of the solvents [15, 16, 17, 18] have been performed. The internal degrees of freedom of the molecules due to proportion of substituted nueleobases and nucleobase multiple collisions. The formation of any neutral clus­ dimers in solution was determined by IR spectroscopy ters takes place during these multiple collisions. [19, 20] and N M R studies [21, 22]. In general, experi­Through a skimmer the neutral sample molecules and ments have shown that a hydrogen bonded configura­ clusters were transported into the ion source of the tion of nucleobase pairs is more favored in non polar RETOF-MS. Ions, ionic fragments and ionic clusters solvents [23] while a stacked configuration is preferred produced during the desorption into the jet were pre­ in aqueous solutions [24]. These results demonstrate vented from entering the ion source by a positive the strong influence of the solvent on the nucleobase voltage on the source repeller plate. The neutral pair formation. molecules and clusters entering the ion source were To examine the contribution of the nueleobases postionized with multi photon ionization (MUPI). themselves to the forces that cause the formation of Pulsed radiation at variable wavelength was provided definite complementary base pairs the interactions of by the frequency doubled (BBO-crystal) output of an free nueleobases in the gas phase have been investi­ excimer laser (XeCl, LPX100 Lambda Physik Göttin­ gated. We used nueleobases without substituting or gen) pumped dye laser (FL 3002 Lambda Physik G öt­ solvation to exclude solvent effects and side group tingen). The UV laser beam was focused into the ion interactions. We felt that by investigating the free nu- source by a 20 cm fused silica lens. A typical ionization cleobases in the gas phase, the old question can be wavelength used was 260 nm. This wavelength was solved, whether the nueleobases themselves form A-T chosen because all sample molecules absorbed at this and C-G pairs or whether the formation of the Wat- wavelength and the photon energy was sufficient to son-Crick pairs is due to the three dimensional struc­ perform two-photon ionization. The laser intensity ture of the DNA or other external effects. The free could be adjusted up to 2 x l0 8 W/cm2 by neutral unsubstituted bases were chosen to exclude any side density filters. The positive ions produced by M U PI group interactions, as they will be shown to influence postionization were separated and detected in the the nucleobase pair formation decisively. RETOF-MS with a typical fwhm resolution of ca. Nucleosides, such as adenosine (Ad), deoxythy­ 3000 at mass 300. Each spectrum represents the sum midine (Td), cytosine (Cd) and guanosine (Gd) differ of 25 spectra recorded using a 200 MHz transient from the nueleobases by addition of a ribose molecule digitizer (Le Croy). to the N 1 atom at the pyrimidine bases or to the N 9 Sample preparation was maintained to avoid any atom at the purine bases. As will be shown, the cluster dimer formation of the sample molecules before desorp­ behavior of gaseous nucleosides differs decisively from tion. The samples were used without further purifi­ 778 M. Dey et al. ■ Pair Formation of Free Nucleobases in the Gas Phase cation as provided by the manufacturer (Serva Chem­ two photons and not three or more. The wavelength icals, Heidelberg). Sample preparation was performed of the ionizing laser was adjusted to significant ioniza­ without any solvents or additional chemicals, but by tion without fragmentation for all four nucleobases. mixing the samples in a mortar and compressing them 260 nm was found to be a wavelength at which all four into thin layers. The pure nucleobase or mononu­ nucleobases could be ionized by absorbing two pho­ cleoside samples were introduced to the desorption tons.
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