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- Publisher Website: 10.1021/bi0115075
- Scopus: eid_2-s2.0-0037066105
- PMID: 11876654
- WOS: WOS:000174387500020
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Article: Potent gene-specific inhibitory properties of mixed-backbone antisense oligonucleotides comprised of 2′-deoxy-2′-fluoro-D-arabinose and 2′-deoxyribose nucleotides
Title | 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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Authors | |
Issue Date | 2002 |
Publisher | American Chemical Society. The Journal's web site is located at http://pubs.acs.org/biochemistry |
Citation | Biochemistry, 2002, v. 41 n. 10, p. 3457-3467 How to Cite? |
Abstract | 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 EC 50 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. |
Persistent Identifier | http://hdl.handle.net/10722/167752 |
ISSN | 2023 Impact Factor: 2.9 2023 SCImago Journal Rankings: 1.042 |
ISI Accession Number ID | |
References |
DC Field | Value | Language |
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dc.contributor.author | Lok, CN | en_US |
dc.contributor.author | Viazovkina, E | en_US |
dc.contributor.author | Min, KL | en_US |
dc.contributor.author | Nagy, E | en_US |
dc.contributor.author | Wilds, CJ | en_US |
dc.contributor.author | Damha, MJ | en_US |
dc.contributor.author | Parniak, MA | en_US |
dc.date.accessioned | 2012-10-08T03:11:02Z | - |
dc.date.available | 2012-10-08T03:11:02Z | - |
dc.date.issued | 2002 | en_US |
dc.identifier.citation | Biochemistry, 2002, v. 41 n. 10, p. 3457-3467 | en_US |
dc.identifier.issn | 0006-2960 | en_US |
dc.identifier.uri | http://hdl.handle.net/10722/167752 | - |
dc.description.abstract | 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 EC 50 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. | en_US |
dc.language | eng | en_US |
dc.publisher | American Chemical Society. The Journal's web site is located at http://pubs.acs.org/biochemistry | en_US |
dc.relation.ispartof | Biochemistry | en_US |
dc.subject.mesh | Arabinose - Analogs & Derivatives - Chemistry | en_US |
dc.subject.mesh | Base Sequence | en_US |
dc.subject.mesh | Circular Dichroism | en_US |
dc.subject.mesh | Deoxyribose - Chemistry | en_US |
dc.subject.mesh | Escherichia Coli - Enzymology | en_US |
dc.subject.mesh | Luciferases - Metabolism | en_US |
dc.subject.mesh | Nucleic Acid Conformation | en_US |
dc.subject.mesh | Oligonucleotides, Antisense - Chemistry - Pharmacology | en_US |
dc.subject.mesh | Ribonuclease H - Isolation & Purification - Metabolism | en_US |
dc.title | Potent gene-specific inhibitory properties of mixed-backbone antisense oligonucleotides comprised of 2′-deoxy-2′-fluoro-D-arabinose and 2′-deoxyribose nucleotides | en_US |
dc.type | Article | en_US |
dc.identifier.email | Lok, CN:cnlok@hku.hk | en_US |
dc.identifier.authority | Lok, CN=rp00752 | en_US |
dc.description.nature | link_to_subscribed_fulltext | en_US |
dc.identifier.doi | 10.1021/bi0115075 | en_US |
dc.identifier.pmid | 11876654 | - |
dc.identifier.scopus | eid_2-s2.0-0037066105 | en_US |
dc.relation.references | http://www.scopus.com/mlt/select.url?eid=2-s2.0-0037066105&selection=ref&src=s&origin=recordpage | en_US |
dc.identifier.volume | 41 | en_US |
dc.identifier.issue | 10 | en_US |
dc.identifier.spage | 3457 | en_US |
dc.identifier.epage | 3467 | en_US |
dc.identifier.isi | WOS:000174387500020 | - |
dc.publisher.place | United States | en_US |
dc.identifier.scopusauthorid | Lok, CN=7006410829 | en_US |
dc.identifier.scopusauthorid | Viazovkina, E=6507963057 | en_US |
dc.identifier.scopusauthorid | Min, KL=7201466717 | en_US |
dc.identifier.scopusauthorid | Nagy, E=35345096200 | en_US |
dc.identifier.scopusauthorid | Wilds, CJ=6701808160 | en_US |
dc.identifier.scopusauthorid | Damha, MJ=7007107329 | en_US |
dc.identifier.scopusauthorid | Parniak, MA=7006356357 | en_US |
dc.identifier.issnl | 0006-2960 | - |