BIOINFORMATICS<-->STRUCTURE
Jerusalem, Israel, November 17-21, 1996

Abstract

Conformational analysis of nucleic acid structures: the asymmetric E-loop of 5S RNA

Alexandra Maier, Wolfgang Schulz and Heinz Sklenar

Max Delbrueck Center of Molecular Medicine, Robert-Roessle-Str. 10, 13122 Berlin

maier@iris2.biosim.mdc-berlin.de

The JUMNA (Junction Minimisation of Nucleic Acids) program [1], a helicoidal minimisation algorithm, has been shown to be a versatile tool for structural analysis of nucleic acids and nucleic acid-ligand complexes. Systematic studies on sequence-dependent DNA con- formations [2] have been extended to elements of RNA structures, such as hairpin and internal loops.

In this contribution we present the results for the asymmetric E-loop of the ribosomal 5S RNA with the sequence 

			          67      75   79
				5'-CCUGGUUAGUACC-
				3'-GGACCAUA-AGGG-
				 108           97
This loop is the target for interactions with a zinc finger domain of the transcription factor TFIIIA and of the ribosomal L5 protein. From mutation studies [3,4] it was con- cluded that a unique three-dimensional structure of the E-loop is important for the recognition process.

Our conformational search has led to several local minima structures which differ in the intra- and extrahelical positions of the bases. For the wild-type sequence of Xenopus laevis the lowest energy structure is in excellent agreement with results of NMR studies [5]. The most prominent features of this structure are the triple-paired bases G75/U76/A100 (involving the reversed Hoogsteen U76/A100 pair) and the unusual A77/G99 pair.

References:
[1] Lavery, R., Zakrzewska, K. and Sklenar, H. (1995), Jumna (Junction minimisation of nucleic acids), Comp. Phys. Comm. 91: 135-158
[2] Poncin, M., Hartmann, B. and Lavery, R. (1992), Conformational sub-states in B-DNA, J. Mol. Biol. 226: 775-794
[3] Theunissen, O., Rudt, F., Guddat, U., Mentzel, H. and Pieler, T. (1992), RNA and DNA Bindung Zinc Fingers in Xenopus TFIIIA, Cell 71: 679-690
[4] Rawlings, S. L., Matt, G. D. and Huber, P. W. (1996), Analysis of the Binding of Xenopus Transcription Factor IIIA to Oocyte 5S rRNA and to the 5S rRNA Gene, J. Mol. Biol. 271 (2): 869 - 877
[5] Wimberly, B., Varani, G. and Tinoco, I., Jr. (1993), The Conformation of Loop E of Eukaryotic 5S Ribosomal RNA, Biochemistry 32: 1078-1087

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