Comparative Study of DNA Enzymes and Ribozymes against the Same Full-length Messenger RNA of the Vanilloid Receptor Subtype I

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 oligo...

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Bibliographic Details
Published in:The Journal of biological chemistry 2002-03, Vol.277 (9), p.7099-7107
Main Authors: Kurreck, Jens, Bieber, Birgit, Jahnel, Ricarda, Erdmann, Volker A.
Format: Article
Language:English
Subjects:
Animals
Base Sequence
Binding Sites
Catalysis
DNA - metabolism
Kinetics
Molecular Sequence Data
Oligonucleotides, Antisense - pharmacology
Protein Binding
Rats
Receptors, Drug - chemistry
Ribonuclease H - metabolism
RNA, Catalytic - metabolism
RNA, Messenger - metabolism
Temperature
Time Factors
Transcription, Genetic
vanilloid receptors (type I)
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Summary: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 higherkreact/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.
ISSN:0021-9258
1083-351X
DOI:10.1074/jbc.M107206200