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ISBN: 978-83-60043-10-3 - eurobic9

ISBN: 978-83-60043-10-3 - eurobic9

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Eurobic9, 2-6 September, 2008, Wrocław, Poland<br />

P88. The Influence of pH on the Loop-structure of an Oligonucleotide<br />

Containing Artificial Nucleobases<br />

S. Johannsen a , D. Böhme b , N. Düpre b , J. Müller b , R.K.O. Sigel a<br />

a<br />

Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland<br />

e-mail: silkej@aci.uzh.ch<br />

b<br />

Faculty of Chemistry, Dortmund University of Technology, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany<br />

We synthesised a 17 nt long oligonucleotide including three imidazole moieties as nucleobase surrogates (see<br />

Figure).[1] In the absence of coordinating metal ions the oligonucleotide adopts a hairpin structure and<br />

constitutes a model system for reaction centres in ribozymes exhibiting acid-base catalysis.<br />

For a detailed analysis of the acid-base properties of each imidazole moiety we used pD-dependent 1H-NMR<br />

spectroscopy of the aromatic protons to determine the intrinsic pKa values. Starting in acidic solution, with<br />

increasing pD all imidazole protons shift to higher field, broaden out or even disappear around pD=7 and<br />

become sharper again at higher pD values. Compared to the pKa of imidazole nucleoside 5'-monophosphate<br />

(ImMP), Im8 and Im<strong>10</strong> show an increase in basicity, of up to 0.4 log units. We further calculated the NMR<br />

solution structures of the hairpin at three different pD values: pD=4.7, 7.2 and <strong>10</strong>.2. Two different, but welldefined<br />

loop structures are observed at low and high pD. In contrast, at neutral pD the loop is rather<br />

unstructured. This may result from a structural intermediate between the two loop structures, i.e., the fully<br />

protonated and completely unprotonated form.<br />

Acknowledgement: Financial support by the European ERAnet-Chemistry, the Swiss National Science<br />

Foundation (20EC21-112708 and SNF-Förderungsprofessur PP002-114759 to R.K.O.S.) and the DFG<br />

(JM1750/2-1 and Emmy Noether programme JM1750/1-3, J.M.) is gratefully acknowledged.<br />

References:<br />

[1] J. Müller D. Böhme, P. Lax, M. Morell Cerdà, M. Roitzsch, Chem. Eur. J. 2005, 11, 6246-6253.<br />

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