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Rationally targeted, conformationally-constrained, oxetane modified oligonucleotides are highly efficient gene silencing molecules
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In: Proceedings of National Academy of Sciences, USAArticle in journal (Refereed) Submitted
URN: urn:nbn:se:uu:diva-91711OAI: oai:DiVA.org:uu-91711DiVA: diva2:164533
Available from: 2004-04-26 Created: 2004-04-26Bibliographically approved
In thesis
1. Chemically Modified Oligonucleotides: Synthesis, Physicochemical and Biochemical Properties of their Duplexes with DNA and RNA
Open this publication in new window or tab >>Chemically Modified Oligonucleotides: Synthesis, Physicochemical and Biochemical Properties of their Duplexes with DNA and RNA
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is based on 9 papers dealing with the synthesis, physicochemical and biochemical properties of two types of chemically modified oligonucleotides which have the potential to down-regulate gene expression: (i) The first set is comprised of antisense oligonucleotides (AONs) conjugated with different chromophores of varying size, charge and π-electron density. Conjugation of the chromophores at the 3'- or 5'-end enhanced the target RNA binding affinity and RNase H recruitment capabilities compared to the native counterpart without changing the global helical conformation of their AON/RNA hybrid duplexes. The 3'-dipyridophenazine (DPPZ) has emerged as the most promising non-toxic chromophore in this series. (ii) The second set encompasses a new class of AONs containing North-East conformationally constrained 1',2'-oxetane-nucleosides. The introduction of oxetane-T and -C units imparts lowering of the Tm by ~ 6º and ~ 3 ºC/modification, respectively, of the AON/RNA hybrids, whereas the incorporation of the corresponding oxetane-A and-G units into AONs did not alter the thermostability in comparison with that of the native hybrid duplex. The oxetane-modified AONs have been found to possess enhanced serum stability compared to that of the native, whereas oxetane-T and -C containing AONs were more endonuclease-resistant than oxetane-A and-G modified AONs. All oxetane-modified mixmer AON/ RNA hybrid duplexes were, however, found to be excellent substrates for RNase H cleavage, which has been analyzed by Michaelis-Menten kinetics. The oxetane-modified mixmer AONs have shown effective down-regulation of the proto-oncogene c-myb mRNA in the K562 human leukemia cells, which was analyzed by QRT-PCR and Western Blot. Based on the amount of AON uptake after delivery, determined by slot blot, it was apparent that the oxetane-modified AONs are 5-6 times more effective antisense agents than the corresponding isosequential phosphorothioate analogues. The electrochemical assay based on sensitive nucleic acid mediated charge transport (CT) has revealed that the presence of oxetane-T unit causes more stacking perturbations in a DNA/DNA duplex than in a DNA/RNA duplex.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2004. 56 p.
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 973
Bioorganic chemistry, Antisense oligonucleotides, Dipyridophenazine, Oxetane, RNase H, Gene down-regulation, DNase 1, Charge transport, Bioorganisk kemi
National Category
Organic Chemistry
urn:nbn:se:uu:diva-4247 (URN)91-554-5957-9 (ISBN)
Public defence
2004-05-21, Floor 3, C10: 301, Biomedical Centre (BMC), Uppsala, 13:30
Available from: 2004-04-26 Created: 2004-04-26Bibliographically approved

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