Nucleic Acids Research, Vol 24, Issue 14 2679-2684, Copyright © 1996 by Oxford University Press
P Hendry and M McCall
RNA substrates which form relatively short helices I and III with
hammerhead ribozymes are generally cleaved more rapidly than substrates
which create longer binding helices. We speculated that for optimum
cleavage rates, one of the helices needed to be relatively weak. To
identify this helix, a series of ribozymes and substrates of varying
lengths were made such that in the complex, helices I and III consisted of
5 and 10 bp respectively or vice versa. In two independent systems,
substrates in the complexes with the shorter helix I and longer helix III
were cleaved one to two orders of magnitude more rapidly than those in the
complexes with the longer helix I and shorter helix III. Similar results
were obtained whether the numbers of base pairs in helices I and III were
limited either by the length of the hybridizing arms of the ribozyme or the
length of the substrate. The phenomenon was observed for both all-RNA and
DNA armed ribozymes. Thus, a relatively short helix I is required for fast
cleavage rates in pre-formed hammer- head ribozyme-substrate complexes.
When helix III has 10 bp, the optimum length for helix I is approximately 5
bp.
ARTICLES
Unexpected anisotropy in substrate cleavage rates by asymmetric hammerhead ribozymes
CSIRO, Division of Biomolecular Engineering, North Ryde, NSW, Australia.
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