How Folding of Single RNA Molecules

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How Folding of Single RNA Molecules Leads to
Biological Function
Nils G. Walter, Single Molecule Analysis Group,
Department of Chemistry, University of Michigan
Non-coding RNA has been discovered to play an
ever more important role in all aspects of
replication, modification, processing, and
regulation of genetic information. Such RNA
molecules undergo large structural changes. Our
research aims to understanding the interplay
between these structural changes and RNA function
in the chemistry of life. We have used
fluorescence microscopy techniques to monitor
structural changes in the large VS ribozyme, one
RNA molecule at a time. The VS ribozyme is found
in parasites of bread mold and functions to
site-specifically cleave itself as part of the
parasites replication cycle.

Cy5 signal
We observe distance changes between Cy3 and Cy5
fluorophores chemically coupled to single VS RNA
molecules that are attached to a surface and
immersed in aqueous solution.
Cy3 signal
35 ?
96 ?
Analysis of many data sets like the one depicted
above shows that the VS ribozyme exhibits dynamic
hierarchical folding. Dynamic formation of a
central kissing loop is required, but only
partially rate-limiting for catalysis. Our
results invoke a model whereby the VS ribozyme
kinetically selects the distal downstream
substrate for cleavage before the proximal
upstream substrate, thus facilitating multimeric
RNA replication. A paper is currently submitted
for review.