An Unusual Structure Formed by Antisense-Target RNA Binding Involves an Extended Kissing Complex with a Four-Way Junction and a Side-by-Side Helical Alignment.

Published in: RNA vol. 6, pp. 311-324 (March, 2000):

"An Unusual Structure Formed by Antisense-Target RNA Binding Involves an Extended Kissing Complex with a Four-Way Junction and a Side-by-Side Helical Alignment."

Fabrice A. Kolb ¹, Charlotta Malmgren ³, Eric Westhof ¹, Chantel Ehresmann ¹, Bernard Ehresmann ¹, E. Gerhart H. Wagner ² and Pascale Romby ¹

¹UPR 9002 du Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 15 rue R. Descartes, Strasbourg cedex, France
²Department of Microbiology, SLU (Swedish University of Agricultural Sciences), Genetikvägen 5, S-75007 Uppsala, Sweden
³Department of Microbiology, Biomedical Center, Uppsala University, S-751 23 Uppsala, Sweden

Abstract:

The antisense RNA CopA binds to the leader region of the repA mRNA (target: CopT). Previous studies on CopA-CopT pairing in vitro showed that the dominant product of antisense RNA-mRNA binding is not a full RNA duplex. We have studied here the structure of CopA-CopT complex, combining chemical and enzymatic probing and computer graphic modeling. CopI, a truncated derivative of CopA unable to bind CopT stably, was also analyzed. We show here that after initial loop-loop interaction (kissing), helix propagation resulted in an extended kissing complex that involves the formation of two intermolecular helices. By introducing mutations (base-pair inversions) into the upper stem regions of CopA and CopT, the boundaries of the two newly formed intermolecular helices were delimited. The resulting extended kissing complex represents a new type of four-way junction structure that adopts an asymmetrical X-shaped conformation formed by two helical domains, each one generated by coaxial stacking of two helices. This structure motif induces a side-by-side alignment of two long intramolecular helices that, in turn, facilitates the formation of an additional intermolecular helix that greatly stabilizes the inhibitory CopA-CopT RNA complex. This stabilizer helix cannot form in CopI-CopT complexes due to absence of the sequences involved. The functional significance of the three-dimensional models of the extended kissing complex (CopI-CopT) and the stable complex (CopA-CopT) are discussed.

Top of Page - Euchromatin Network - Current Research - Forums - Other Sites - Future Events -

For Further Information and Feedback:
E-mail: matcog@ix.netcom.com

euchromatin: "the most active portion of the genome within the cell nucleus."