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Issue 27, 2013
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Vibrational signatures of Watson–Crick base pairing in adenine–thymine mimics

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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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Supplementary files

Article information


Submitted
24 Jan 2013
Accepted
08 May 2013
First published
10 Jun 2013

Phys. Chem. Chem. Phys., 2013,15, 11520-11530
Article type
Paper

Vibrational signatures of Watson–Crick base pairing in adeninethymine 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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