Issue 27, 2013
From the journal:

Physical Chemistry Chemical Physics

Vibrational signatures of Watson–Crick base pairing in adenine–thymine mimics†

Yevgeniy Nosenko,‡*a   Maksim Kunitski,a   Tina Stark,b   Michael Göbel,b   Pilarisetty Tarakeshwarc  and  Bernhard Brutschy*a  

* Corresponding authors

a Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt/Main, Germany
E-mail: nosenko@chemie.uni-kl.de, brutschy@chemie.uni-frankfurt.de

b Institut für Organische Chemie und Chemische Biologie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt/Main, Germany

c Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA

Abstract

The vibrational fingerprints of hydrogen-bonding associated with the adenine–thymine (A–T) Watson–Crick (WC) base pair have been identified in an infrared study of the A–T mimics 4-aminopyrimidine–1-methylthymine (4APM–1MT) and 4-aminopyrimidine–6-methyl-4-pyrimidinone (4APM–M4PMN) in the gas-phase. The IR vibrational spectra were measured via a double resonance scheme utilizing femtosecond multiphoton ionization. The changes in the molecular structure, anharmonic vibrational parameters, and the assignment of the observed vibrational spectra in the NH/CH stretch region were investigated by carrying out high-level theoretical calculations of the anharmonic spectra. The experimental observations and theoretical calculations indicate that the hydrogen bonds associated with WC base-pairing are relatively stronger than those associated with reverse WC (rWC) base pairing. This is manifested in a more pronounced red-shift of the H-bonded vibrational modes associated with the WC as compared with the rWC base-pairing. An analysis of the factors contributing to the anharmonicity of the vibrational modes associated with H-bonding reveals that the magnitude of the off-diagonal anharmonic coupling of the H-bonded –NH2 stretch and the –NH2 bend is much smaller in WC base-pairing than in the corresponding rWC base-pairing. The chemical and biological implications of these results, especially in the context of using vibrational spectroscopy as a tool for identifying the signatures of nucleotide base vibrations is addressed.

Graphical abstract: Vibrational signatures of Watson–Crick base pairing in adenine–thymine mimics

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Article information

DOI
https://doi.org/10.1039/C3CP50337B
Article type
Paper
Submitted
24 Jan 2013
Accepted
08 May 2013
First published
10 Jun 2013

Phys. Chem. Chem. Phys., 2013,15, 11520-11530

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Vibrational signatures of Watson–Crick base pairing in adenine–thymine mimics

Y. Nosenko, M. Kunitski, T. Stark, M. Göbel, P. Tarakeshwar and B. Brutschy, Phys. Chem. Chem. Phys., 2013, 15, 11520 DOI: 10.1039/C3CP50337B

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