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Title: 4'- C -Methoxy-2-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing

Abstract

We designed novel 4'-modified 2'-deoxy-2'-fluorouridine (2'-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4'-C-methoxy (4'-OMe) as the alpha (C4'α) or beta (C4'β) epimers. The C4'α epimer was synthesized by a stereoselective route in six steps; however, both α and β epimers could be obtained by a nonstereoselective approach starting from 2'-F U. 1H NMR analysis and computational investigation of the α-epimer revealed that the 4'-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-epimer led to significant destabilization. Both 4'-OMe epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4'-OMe substituent and the vicinal 5'- and 3'-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs containing several C4'α-epimer monomers in the sense or antisense strands triggered RNAi-mediated gene silencing with efficiencies comparable to that of 2'-F U.

Authors:
 [1];  [2];  [2];  [1];  [2];  [3];  [1];  [2];  [1];  [2]; ORCiD logo [1];  [2];  [2];  [2];  [2];  [2]; ORCiD logo [2];  [3];  [2]; ORCiD logo [1]
  1. Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
  2. Alnylam Pharmaceuticals, 300 Third Street, Cambridge, Massachusetts 02142, United States
  3. Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
FOREIGN
OSTI Identifier:
1410690
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of the American Chemical Society; Journal Volume: 139; Journal Issue: 41
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 60 APPLIED LIFE SCIENCES

Citation Formats

Malek-Adamian, Elise, Guenther, Dale C., Matsuda, Shigeo, Martínez-Montero, Saúl, Zlatev, Ivan, Harp, Joel, Burai Patrascu, Mihai, Foster, Donald J., Fakhoury, Johans, Perkins, Lydia, Moitessier, Nicolas, Manoharan, Rajar M., Taneja, Nate, Bisbe, Anna, Charisse, Klaus, Maier, Martin, Rajeev, Kallanthottathil G., Egli, Martin, Manoharan, Muthiah, and Damha, Masad J.. 4'- C -Methoxy-2-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing. United States: N. p., 2017. Web. doi:10.1021/jacs.7b07582.
Malek-Adamian, Elise, Guenther, Dale C., Matsuda, Shigeo, Martínez-Montero, Saúl, Zlatev, Ivan, Harp, Joel, Burai Patrascu, Mihai, Foster, Donald J., Fakhoury, Johans, Perkins, Lydia, Moitessier, Nicolas, Manoharan, Rajar M., Taneja, Nate, Bisbe, Anna, Charisse, Klaus, Maier, Martin, Rajeev, Kallanthottathil G., Egli, Martin, Manoharan, Muthiah, & Damha, Masad J.. 4'- C -Methoxy-2-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing. United States. doi:10.1021/jacs.7b07582.
Malek-Adamian, Elise, Guenther, Dale C., Matsuda, Shigeo, Martínez-Montero, Saúl, Zlatev, Ivan, Harp, Joel, Burai Patrascu, Mihai, Foster, Donald J., Fakhoury, Johans, Perkins, Lydia, Moitessier, Nicolas, Manoharan, Rajar M., Taneja, Nate, Bisbe, Anna, Charisse, Klaus, Maier, Martin, Rajeev, Kallanthottathil G., Egli, Martin, Manoharan, Muthiah, and Damha, Masad J.. Fri . "4'- C -Methoxy-2-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing". United States. doi:10.1021/jacs.7b07582.
@article{osti_1410690,
title = {4'- C -Methoxy-2-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing},
author = {Malek-Adamian, Elise and Guenther, Dale C. and Matsuda, Shigeo and Martínez-Montero, Saúl and Zlatev, Ivan and Harp, Joel and Burai Patrascu, Mihai and Foster, Donald J. and Fakhoury, Johans and Perkins, Lydia and Moitessier, Nicolas and Manoharan, Rajar M. and Taneja, Nate and Bisbe, Anna and Charisse, Klaus and Maier, Martin and Rajeev, Kallanthottathil G. and Egli, Martin and Manoharan, Muthiah and Damha, Masad J.},
abstractNote = {We designed novel 4'-modified 2'-deoxy-2'-fluorouridine (2'-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4'-C-methoxy (4'-OMe) as the alpha (C4'α) or beta (C4'β) epimers. The C4'α epimer was synthesized by a stereoselective route in six steps; however, both α and β epimers could be obtained by a nonstereoselective approach starting from 2'-F U. 1H NMR analysis and computational investigation of the α-epimer revealed that the 4'-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-epimer led to significant destabilization. Both 4'-OMe epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4'-OMe substituent and the vicinal 5'- and 3'-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs containing several C4'α-epimer monomers in the sense or antisense strands triggered RNAi-mediated gene silencing with efficiencies comparable to that of 2'-F U.},
doi = {10.1021/jacs.7b07582},
journal = {Journal of the American Chemical Society},
number = 41,
volume = 139,
place = {United States},
year = {Fri Oct 06 00:00:00 EDT 2017},
month = {Fri Oct 06 00:00:00 EDT 2017}
}