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Structural comparison of oligoribonucleotides and their 2 -Deoxy-2 -fluoro analogs by heteronuclear NMR spectroscopy

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1997

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Reif, Bernd
Schwalbe, Harald
Griesinger, Christian
Wörner, Karlheinz
Jahn-Hofmann, Kerstin
Engels, Joachim W.
Bermel, Wolfgang

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Helvetica Chimica Acta. 1997, 80(6), pp. 1952-1971. ISSN 0018-019X. eISSN 1522-2675. Available under: doi: 10.1002/hlca.19970800614

Zusammenfassung

1-(2-Deoxy-2-fluororibofuranosyl)pyrimidines were synthesized and incorporated into an RNA oligonucleotide to give 5-r[CfGCf(UfUfCfG)GCfG]-3 (Cf: short form of Cd2f2 = 2-deoxy-2-fluorocytidine; Uf: short form of Ud2f2 = 2-deoxy-2-fluorouridine). The oligomer was investigated by means of UV, CD, and NMR spectroscopy to address the question of how F-labels can substitute 13C-labels in the ribose ring. Through-space (NOE) and through-bond (scalar couplings) experiments were performed that make use of the ameliorated chemical-shift dispersion induced by 19F as an alternative heteronucleus. A comparison of the structures of fluorinated vs. unmodified oligomer is given. It turns out that the fluorinated oligonucleotide exists in a 14:3 equilibrium between a hairpin and a duplex conformation, in contrast to the unmodified oligonucleotide which predominantly adopts the hairpin conformation. Furthermore, the fluorinated hairpin structure adopts two distinct conformations that differ in the sugar conformation of the U and C nucleoside units, as detected by the 19F-NMR chemical shifts. The role of the 2-OH group as stabilizing element in RNA secondary structure is discussed.

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540 Chemie

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ISO 690REIF, Bernd, Valentin WITTMANN, Harald SCHWALBE, Christian GRIESINGER, Karlheinz WÖRNER, Kerstin JAHN-HOFMANN, Joachim W. ENGELS, Wolfgang BERMEL, 1997. Structural comparison of oligoribonucleotides and their 2 -Deoxy-2 -fluoro analogs by heteronuclear NMR spectroscopy. In: Helvetica Chimica Acta. 1997, 80(6), pp. 1952-1971. ISSN 0018-019X. eISSN 1522-2675. Available under: doi: 10.1002/hlca.19970800614
BibTex
@article{Reif1997Struc-9561,
  year={1997},
  doi={10.1002/hlca.19970800614},
  title={Structural comparison of oligoribonucleotides and their 2 -Deoxy-2 -fluoro analogs by heteronuclear NMR spectroscopy},
  number={6},
  volume={80},
  issn={0018-019X},
  journal={Helvetica Chimica Acta},
  pages={1952--1971},
  author={Reif, Bernd and Wittmann, Valentin and Schwalbe, Harald and Griesinger, Christian and Wörner, Karlheinz and Jahn-Hofmann, Kerstin and Engels, Joachim W. and Bermel, Wolfgang}
}
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