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J. Biol. Chem., Vol. 277, Issue 9, 7099-7107, March 1, 2002
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From the Free University Berlin, Institute of Biochemistry,
Thielallee 63, 14195 Berlin, Germany
The efficiencies of 32 antisense
oligodeoxynucleotides, 35 DNA enzymes and 6 ribozymes to bind and
cleave the full-length messenger RNA of the vanilloid receptor subtype
I were analyzed. Systematic screening of the mRNA revealed that
good accessibility of a putative cleavage site for antisense
oligodeoxynucleotides is a necessary but not a sufficient prerequisite
for efficient DNA enzymes. Comparison of DNA enzymes and ribozymes
against the same target sites revealed: 1) DNA enzymes were more active
with longer recognition arms (9 nucleotides on either side), whereas ribozymes revealed higher activities with shorter recognition arms (7 nucleotides on either side). 2) It does not only depend on the target
site but also on the enzyme sequence, whether a DNA enzyme or a
ribozyme is more active. 3) The most efficient DNA enzyme found in this
study had an ~15-fold higher reaction rate,
kreact, and a 100-fold higher
kreact/Km under single turnover conditions compared with the fastest ribozyme. DNA enzymes as
well as ribozymes showed significant activity under multiple turnover conditions, the DNA enzymes again being more active. We
therefore conclude that DNA enzymes are an inexpensive, very stable and
active alternative to ribozymes for the specific cleavage of long RNA molecules.
Comparative Study of DNA Enzymes and Ribozymes against the Same
Full-length Messenger RNA of the Vanilloid Receptor Subtype I*
*
This work was supported by Bundesministerium für
Bildung und Forschung Grant 01GG9818/0 and the Fonds of the Chemische
Industrie e. V.The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
To whom correspondence should be addressed. Tel.:
49-30-83-85-60-02; Fax: 49-30-83-85-64-13; E-mail:
erdmann@chemie.fu-berlin.de.
Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.
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