4-Aminobenzimidazole-1-methylthymine: a model for investigating Hoogsteen base-pairing between adenine and thymine.

Yevgeniy Nosenko, Maksim Kunitski, Tina Stark, Michael Göbel, Pilarisetty Tarakeshwar, Bernhard Brutschy

Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Frankfurt/Main, Germany.

The journal of physical chemistry. A 2011 Oct 20

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We report the infrared spectrum of the 4-aminobenzimidazole-1-methylthymine (4ABI:1MT) heterodimer, detected by femtosecond multiphoton ionization. Based on calculations of both the harmonic and the anharmonic frequencies, the observed vibrational spectrum is assigned to a structure that mimics the Hoogsteen base pairing of adenine and thymine. A notable observation made in the course of this study is that there is a significant imbalance in the observed strengths of the H-bonds. While the N···H-N bond reveals a large red shift of >700 cm(-1) for the NH stretch frequency, the N-H···O bond is characterized by only a 50 cm(-1) shift. The importance of this observation in the formation of Hoogsteen duplexes by thymine-based oligonucleotides is discussed.

Citation

Yevgeniy Nosenko, Maksim Kunitski, Tina Stark, Michael Göbel, Pilarisetty Tarakeshwar, Bernhard Brutschy. 4-Aminobenzimidazole-1-methylthymine: a model for investigating Hoogsteen base-pairing between adenine and thymine. The journal of physical chemistry. A. 2011 Oct 20;115(41):11403-11