N3‘→P5‘ Oligodeoxyribonucleotide Phosphoramidates:  A New Method of Synthesis Based on a Phosphoramidite Amine-Exchange Reaction

Nelson, Jeffrey S.; Fearon, Karen L.; Nguyen, Mark Q.; McCurdy, Sarah N.; Frediani, Jeff E.; Foy, Michael F.; Hirschbein, Bernard L.

doi:10.1021/jo970801t

Cited by 45 publications

(38 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1) were purchased either from Xeragon (Zürich) and Eurogentec (Brussels) or were synthesized on an Expedite 8908 synthesizer (Applied Biosystems). Oligonucleotide N3Ј 3 P5Ј deoxyphosphoramidates were prepared as described (20,21). All oligonucleotides were purified by electrophoresis on denaturing 20% polyacrylamide, 7 M urea gels and desalted on Sephadex G-25 spin columns.…”

Section: Methodsmentioning

confidence: 99%

“…Synthesis of N3Ј 3 P5Ј phosphoramidate oligodeoxynucleotides (NP-DNA), which are resistant to digestion by snake venom phosphodiesterase and by nucleases in HeLa cell nuclear extract, has been described (20,21). NMR experiments showed that a NP-DNA duplex d(CGCGAATTCGCG) 2 adopts an A-type helix conformation in solution (22), suggesting that NP-DNA could be used as RNA mimetics.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Loop–loop interaction of HIV-1 TAR RNA with N3′ → P5′ deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription

Darfeuille

Arzumanov

Gryaznov

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

A hairpin RNA aptamer has been identified by in vitro selection against the transactivation-responsive element (TAR) of HIV-1. A nuclease-resistant N3 3 P5 phosphoramidate isosequential analog of this aptamer also folds as a hairpin and forms with TAR a loop-loop ''kissing'' complex with a binding constant in the low nanomolar range as demonstrated by electrophoretic mobilityshift assays and surface plasmon resonance experiments. The key structural determinants, which contribute to the stability of the RNA aptamer-TAR complex, loop complementarity and the GA residues closing the aptamer loop, remain crucial for the N3 3 P5 aptamer-TAR complex. Moreover, the N3 3 P5 phosphoramidate aptamer specifically interferes with the binding of a peptide derived from the transactivator protein (Tat) peptide to TAR and selectively inhibits the Tat-mediated transcription in an in vitro assay, which marks this nuclease-resistant aptamer as a relevant candidate for experiments in cells.

show abstract

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Loop–loop interaction of HIV-1 TAR RNA with N3′ → P5′ deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription

Darfeuille

Arzumanov

Gryaznov

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Oligonucleotide analogues with N3Ј-P5Ј np linkages were synthesized as described (12)(13)(14)(15). Acridine and psoralen-5Ј modified oligonucleotides were prepared as reported (refs.…”

Section: Methodsmentioning

confidence: 99%

Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides

Faria

Wood

Perrouault

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

139

View full text Add to dashboard Cite

Triple-helix-forming oligonucleotides (TFOs) bind in the major groove of double-stranded DNA at oligopyrimidine⅐oligopurine sequences and therefore are candidate molecules for artificial gene regulation, in vitro and in vivo. We recently have described oligonucleotide analogues containing N3-P5 phosphoramidate (np) linkages that exhibited efficient inhibition of transcription elongation in vitro. In the present work we provide conclusive evidence that np-modified TFOs targeted to the HIV-1 polypurine tract (PPT) sequence can inhibit transcriptional elongation in cells, either in transient or stable expression systems. The same constructs were used in transient expression assays (target sequence on transfected plasmid) and in the generation of stable cell lines (target sequence integrated into cellular chromosomes). In both cases the only distinguishable feature between the cellular systems is the presence of an insert containing the wild-type PPT͞HIV-1 sequence, a mutated version with two mismatches, or the absence of the insert altogether. The inhibitory action induced by np-TFOs was restricted to the cellular systems containing the complementary wild-type PPT͞HIV-1 target, and consequently can be attributed only to a triple-helix-mediated mechanism. As a part of this study we also have applied an imaging technique to quantitatively investigate the dynamics of TFO-mediated specific gene silencing in single cells.

show abstract

“…The four 3Ј-(trityl)amino-2Ј, 3Ј-dideoxynucleoside 5Ј-N, N-diisopropyl(2-cyanoethyl) phosphoramidites required for the synthesis of N3Ј Ǟ P5Ј phosphoramidatemodified ODNs were prepared as described (Nelson et al, 1997)…”

Section: Oligomersmentioning

confidence: 99%

Potent Inhibitory Activity of Chimeric Oligonucleotides Targeting Two Different Sites of Human Telomerase

Matthes¹,

Lehmann²,

Stulich³

et al. 2005

Oligonucleotides

View full text Add to dashboard Cite

Suppression of telomerase activity in tumor cells has been considered as a new anticancer strategy.Here, we present chimeric oligonucleotides (chimeric ODNs) as a new type of telomerase inhibitor that contains differently modified oligomers to address two different sites of telomerase: the RNA template and a suggested protein motif. We have shown previously that phosphorothioate-modified oligonucleotides (PS ODNs) interact in a length-dependent rather than in a sequence-dependent manner, presumably with the protein part of the primer-binding site of telomerase, causing strong inhibition of telomerase. In the present study, we demonstrate that extensions of these PS ODNs at their 3-ends with an antisense oligomer partial sequence covering 11 bases of the RNA template cause significantly increased inhibitory activity, with IC 50 values between 0.60 and 0.95 nM in a Telomeric Repeat Amplification Protocol (TRAP) assay based on U-87 cell lysates. The enhanced inhibitory activity is observed regardless of whether the antisense part is modified (phosphodiester, PO; 2-O-methylribosyl, 2-OMe/PO; phosphoramidate, PAM). However, inside intact U-87 cells, these modifications of the antisense part proved to be essential for efficient telomerase inhibition 20 hours after transfection. In particular, the chimeric ODNs containing PAM or 2-OMe/PO modifications, when complexed with lipofectin, were most efficient telomerase inhibitors (ID 50 ‫؍‬ 0.04 and 0.06 M, respectively). In conclusion, ODNs of this new type emerged as powerful inhibitors of human telomerase and are, therefore, promising candidates for further investigations of the anticancer strategy of telomerase inhibition.

show abstract

N3‘→P5‘ Oligodeoxyribonucleotide Phosphoramidates: A New Method of Synthesis Based on a Phosphoramidite Amine-Exchange Reaction

Cited by 45 publications

References 20 publications

Loop–loop interaction of HIV-1 TAR RNA with N3′ → P5′ deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription

Loop–loop interaction of HIV-1 TAR RNA with N3′ → P5′ deoxyphosphoramidate aptamers inhibits in vitro Tat-mediated transcription

Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides

Potent Inhibitory Activity of Chimeric Oligonucleotides Targeting Two Different Sites of Human Telomerase

Contact Info

Product

Resources

About