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Potent Gene-Specific Inhibitory Properties of Mixed-Backbone Antisense Oligonucleotides Comprised of 2‘-Deoxy-2‘-fluoro-d-arabinose and 2‘-Deoxyribose Nucleotides,

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    Potent Gene-Specific Inhibitory Properties of Mixed-Backbone Antisense Oligonucleotides Comprised of 2‘-Deoxy-2‘-fluoro-d-arabinose and 2‘-Deoxyribose Nucleotides†,#
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    Lady Davis Institute for Medical Research, Department of Medicine, and Department of Chemistry, McGill University, Montreal, Quebec PQ, Canada H3A 2K6
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    Biochemistry

    Cite this: Biochemistry 2002, 41, 10, 3457–3467
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    https://doi.org/10.1021/bi0115075
    Published February 13, 2002
    Copyright © 2002 American Chemical Society
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    Abstract

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    Phosphorothioate deoxyribonucleotides (PS-DNA) are among the most widely used antisense inhibitors. PS-DNA exhibits desirable properties such as enhanced nuclease resistance, improved bioavailability, and the ability to induce RNase H mediated degradation of target RNA. Unfortunately, PS-DNA possesses a relatively low binding affinity for target RNA that impacts on its potency in antisense applications. We recently showed that phosphodiester-linked oligonucleotides comprised of 2‘-deoxy-2‘-fluoro-d-arabinonucleic acid (FANA) exhibit both high binding affinity for target RNA and the ability to elicit RNase H degradation of target RNA [Damha et al. (1998) J. Am. Chem. Soc.120, 12976]. In the present study, we evaluated the antisense activity of phosphorothioate-linked FANA oligonucleotides (PS-FANA). Oligonucleotides comprised entirely of PS-FANA were somewhat less efficient in directing RNase H cleavage of target RNA as compared to their phosphorothioate-linked DNA counterparts, and showed only weak antisense inhibition of cellular target expression. However, mixed-backbone oligomers comprised of PS-FANA flanking a central core of PS-DNA were found to possess potent antisense activity, inhibiting specific cellular gene expression with EC50 values of less than 5 nM. This inhibition was a true antisense effect, as indicated by the dose-dependent decrease in both target protein and target mRNA. Furthermore, the appearance of mRNA fragments was consistent with RNase H mediated cleavage of the mRNA target. We also compared a series of PS-[FANA-DNA-FANA] mixed-backbone oligomers of varying PS-DNA core sizes with the corresponding 2‘-O-methyl oligonucleotide chimeras, i.e., PS-[2‘meRNA-DNA-2‘meRNA]. Both types of oligomers showed very similar binding affinities toward target RNA. However, the antisense potency of the 2‘-O-methyl chimeric compounds was dramatically attenuated with decreasing DNA core size, whereas that of the 2‘-fluoroarabino compounds was essentially unaffected. Indeed, a PS-FANA oligomer containing a single deoxyribonucleotide residue core retained significant antisense activity. These findings correlated exactly with the ability of the various chimeric antisense molecules to elicit RNase H degradation of the target RNA in vitro, and suggest that this mode of inhibition is likely the most important determinant for potent antisense activity.

    Copyright © 2002 American Chemical Society

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    †

     This work was supported in part by a grant from the Canadian Institutes of Health Research (M.A.P. and M.J.D.) and funding from Anagenis, Inc. [Montreal, QC; supported by MedTech Partners and Transfer Technology Commercialization Capital (T2C2/BIO)]. M.A.P. and M.J.D. are principals in Anagenis, Inc. During the conduct of this research, M.A.P. was a CIHR Senior Scientist and an International Research Scholar of the Howard Hughes Medical Institute.

    #

     This work is dedicated to Professor David N. Harpp on the occasion of his 65th birthday.

    ‡

     Lady Davis Institute for Medical Research.

    §

     Department of Medicine.

    ‖

     Department of Chemistry.

    *

     Corresponding authors. M.J.D.:  Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC, Canada H3A-2K6. Tel:  (514) 398-7552, Fax:  (514) 398-3797, Email:  masad.damha@ mcgill.ca.

    ⊥

     Present address:  University of Pittsburgh School of Medicine, Department of Medicine, Division of Infectious Diseases, Scaife Hall, Room S818D, 3550 Terrace St., Pittsburgh, PA 15261. Tel:  (412) 648-1927, Fax:  (412) 383-7982, Email:  [email protected].

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    Biochemistry

    Cite this: Biochemistry 2002, 41, 10, 3457–3467
    Click to copy citationCitation copied!
    https://doi.org/10.1021/bi0115075
    Published February 13, 2002
    Copyright © 2002 American Chemical Society
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