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Selection, design, and characterization of a new potentially therapeutic ribozyme

Published online by Cambridge University Press:  13 February 2002

SHAWN P. ZINNEN
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
KRISTAL DOMENICO
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
MIKE WILSON
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
BRENT A. DICKINSON
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
AMBER BEAUDRY
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
VICTOR MOKLER
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
ANDREW T. DANIHER
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
ALEX BURGIN
Affiliation:
Department of Biology, San Diego State University, San Diego, California 92182-4614, USA
LEONID BEIGELMAN
Affiliation:
Ribozyme Pharmaceuticals Incorporated, Boulder, Colorado 80301, USA
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Abstract

An in vitro selection was designed to identify RNA-cleaving ribozymes predisposed for function as a drug. The selection scheme required the catalyst to be trans-acting with phosphodiesterase activity targeting a fragment of the Kras mRNA under simulated physiological conditions. To increase stabilization against nucleases and to offer the potential for improved functionality, modified sequence space was sampled by transcribing with the following NTPs: 2′-F-ATP, 2′-F-UTP, or 2′-F-5-[(N-imidazole-4-acetyl) propylamine]-UTP, 2′-NH2-CTP, and GTP. Active motifs were identified and assessed for their modified NMP and divalent metal dependence. The minimization of the ribozyme's size and the ability to substitute 2′-OMe for 2′-F and 2′-NH2 moieties yielded the motif from these selections most suited for both nuclease stability and therapeutic development. This motif requires only two 2′-NH2-Cs and functions as a 36-mer. Its substrate sequence requirements were determined to be 5′–Y-G-H–3′. Its half-life in human serum is >100 h. In physiologically relevant magnesium concentrations [∼1 mM] its kcat = 0.07 min−1, Km = 70 nM. This report presents a novel nuclease stable ribozyme, designated ZinzymeTM, possessing optimal activity in simulated physiological conditions and ready for testing in a therapeutic setting.

Type
Research Article
Copyright
© 2002 RNA Society

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