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Nucleic Acids Research, 2002, Vol. 30, No. 12 2669-2677
© 2002 Oxford University Press

Solution structure of dAATAA and dAAUAA DNA bulges

Friedrich A. Gollmick1, Mike Lorenz1, Utz Dornberger, Johannes von Langen1, Stephan Diekmann1 and Hartmut Fritzsche*

Institut für Molekularbiologie, Friedrich-Schiller-Universität, Winzerlaer Strasse 10, D-07745 Jena, Germany and 1Institut für Molekulare Biotechnologie e.V., Beutenbergstrasse 11, D-07745 Jena, Germany

The NMR structure analysis is described for two DNA molecules of identical stem sequences with a five base loop containing a pyrimidine, thymin or uracil, in between purines. These five unpaired nucleotides are bulged out and are known to induce a kink in the duplex structure. The dAATAA bulge DNA is kinked between the third and the fourth nucleotide. This contrasts with the previously studied dAAAAA bulge DNA where we found a kink between the fourth and fifth nucleotide. The total kinking angle is ~104° for the dAATAA bulge. The findings were supported by electrophoretic data and fluorescence resonance energy transfer measurements of a similar DNA molecule end-labeled by suitable fluorescent dyes. For the dAAUAA bulge the NMR data result in a similar structure as reported for the dAATAA bulge with a kinking angle of ~87°. The results are discussed in comparison with a rAAUAA RNA bulge found in a group I intron. Generally, the sequence-dependent structure of bulges is important to understand the role of DNA bulges in protein recognition.

* To whom correspondence should be addressed. Tel: +49 3641 657560; Fax: +49 3641 657520; Email: hfri{at}molebio.uni-jena.de


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