A folding control element for tertiary collapse of a group II intron ribozyme

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Abstract

Ribozymes derived from the group II intron ai5γ collapse to a compact intermediate, folding to the native state through a slow, direct pathway that is unperturbed by kinetic traps. Molecular collapse of ribozyme D135 requires high magnesium concentrations and is thought to involve a structural element in domain 1 (D1). We used nucleotide analog interference mapping, in combination with nondenaturing gel electrophoresis, to identify RNA substructures and functional groups that are essential for D135 tertiary collapse. This revealed that the most crucial atoms for compaction are located within a small section of D1 that includes the κ and ζ elements. This small substructure controls specific collapse of the molecule and, in later steps of the folding pathway, it forms the docking site for catalytic D5. In this way, the stage is set for proper active site formation during the earliest steps of ribozyme folding.

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Figure 1: Experimental design.
Figure 2: Summary of interferences and enhancements throughout D135.
Figure 3: Cluster I, the D5 docking site and the coordination loop.
Figure 4: Structural elements crucial for tertiary collapse versus catalysis.
Figure 5: The roles of κ and ζ elements in tertiary collapse versus docking of D5.

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Acknowledgements

We thank O. Fedorova for many helpful discussions and for critically reading the manuscript. We also thank T. Diep for helpful discussions, and we acknowledge G. Drews for excellent technical assistance. This work was supported by US National Institutes of Health grant GM50313 to A.M.P. and by a Schrödinger postdoctoral fellowship (J2332) from the Austrian Science Foundation to C.W. A.M.P. is an Investigator of the Howard Hughes Medical Institute.

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Correspondence to Anna Marie Pyle.

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Supplementary information

Supplementary Fig. 1

Cluster I. (PDF 973 kb)

Supplementary Fig. 2

Cluster II. (PDF 1539 kb)

Supplementary Fig. 3

Cluster III. (PDF 1051 kb)

Supplementary Fig. 4

Mapping Domains 3 and 5. (PDF 1190 kb)

Supplementary Fig. 5

Catalytic activity and compaction. (PDF 361 kb)

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