Abstract
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 spectroscopy1,2,3 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 degradation4,5,6,7,8,9. 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 pathways10. 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 interactions11,12,13.
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References
Fodor, S. P. et al. H/Sub 2/Raman-shifted YAG laser ultraviolet raman spectrometer operating at wavelengths down to 184 nm. J. Raman Spectrosc. 17, 471–475 (1986).
Urabe, H. et al. Collective vibrational modes in molecular assembly of DNA and its application to biological systems. Low frequency raman spectroscopy. J. Chem. Phys. 82, 531–535 (1985).
Cocco, S. & Monasson, R. Theoretical study of collective modes in DNA at ambient temperature. J. Chem. Phys. 112, 10017–10033 (2000).
Brady, B. B., Peteanu, L. A. & Levy, D. H. The electronic spectra of the pyrimidine bases uracil and thymine in a supersonic molecular beam. Chem. Phys. Lett. 147, 538–543 (1988).
Viant, M. R. et al. Infrared laser spectroscopy of uracil in a pulsed slit jet. J. Chem. Phys. 103, 9502– 9505 (1995).
Nir, E. et al. REMPI spectroscopy of jet cooled guanine. J. Am. Chem. Soc. 121, 4896–4897 ( 1999).
Yanson, I. K., Teplitsky, A. B. & Sukhodub, L. F. Molecular interactions in nucleic acids. Biopolymers 18, 1149–1170 (1997).
Dey, M. et al. Base pair formation of free nucleobases and mononucleosides in the gas phase. J. Am. Chem. Soc. 116, 9211 –9215 (1994).
Dey, M., Grotemeyer, J. & Schlag, E. W. Pair formation of free nucleobases and mononucleosides in the gas-phase. Z. Naturforsch. 49A, 776 –784 (1994).
Hutter, M. & Clark, T. On the enhanced stability of the guanine-cytosine base-pair radical cation. J. Am. Chem. Soc. 118, 7574–7577 (1996).
Florian, J., Leszczynski, J., Johnson, B. G. On the intermolecular vibrational modes of the guanine-cytosine, adenine-thymine and formamide-formamide H-bonded dimers. J. Mol. Struct. 349, 421–426 ( 1995).
Shishkin, O., Sponer, J., Hobza, P. Intermolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson-Crick base pairs. J. Mol. Struct. 477, 15–21 (1999).
Santamaria, R. et al. Vibrational spectra of nucleic acid bases and their Watson-Crick pair complexes. J. Comput. Chem. 20, 511 –530 (1999).
Meijer, G. et al. Laser desorption jet-cooling of organic molecules. Cooling characteristics and detection sensitivity. Appl. Phys. B 51, 395–403 (1990).
Schutz, M., Burgi, T. & Leutwyler, S. Intermolecular bonding and vibrations of phenol.H 2O (D2O). J. Chem. Phys. 98, 3763–3777 (1993).
Schmitt, M., Jacoby, C. & Kleinermanns, K. Torsional splitting of the intermolecular vibrations of phenol (H2O)1 and its deuterated isotopomers. J. Chem. Phys. 108, 4486–4495 (1997).
Sponer, J., Leszczynski, J. & Hobza, P. Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. J. Phys. Chem. 100, 1965–1974 (1995).
Hobza, P. et al. Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results. J. Comput. Chem. 18, 1136–1150 ( 1997).
Hobza, P. & Sponer, J. Thermodynamic characteristics for the formation of H-bonded DNA base pairs. Chem. Phys. Lett. 261, 379–384 (1996).
Colson, A. et al. Ab initio molecular orbital calculations on DNA base pair radical ions: Effect of base pairing on proton-transfer energies, electron affinities, and ionization potentials. J. Phys. Chem. 96, 9787–9794 (1992).
Janzen, C. et al. Structure and vibrations of Phenol(H2O)7,8 studied by infrared-ultraviolet and ultraviolet-ultraviolet double-resonance spectroscopy and ab initio theory. J. Chem. Phys. 110, 9898–9907 (1999).
Acknowledgements
This work has been supported by the Deutsche Forschungsgemeinschaft and United States–Israel Binational Science Foundation.
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Nir, E., Kleinermanns, K. & de Vries, M. Pairing of isolated nucleic-acid bases in the absence of the DNA backbone . Nature 408, 949–951 (2000). https://doi.org/10.1038/35050053
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DOI: https://doi.org/10.1038/35050053
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