Cargando…
Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct
A high-resolution solution structure of a stable 42-nt RNA dimeric construct has been derived based on a high number of NMR observables including nuclear overhauser effects (NOEs), J-coupling constants and residual dipolar couplings (RDCs), which were all obtained with isotopically unlabeled molecul...
Autores principales: | , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2010
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978378/ https://www.ncbi.nlm.nih.gov/pubmed/20624819 http://dx.doi.org/10.1093/nar/gkq621 |
_version_ | 1782191253951086592 |
---|---|
author | Podbevsek, Peter Allerson, Charles R. Bhat, Balkrishen Plavec, Janez |
author_facet | Podbevsek, Peter Allerson, Charles R. Bhat, Balkrishen Plavec, Janez |
author_sort | Podbevsek, Peter |
collection | PubMed |
description | A high-resolution solution structure of a stable 42-nt RNA dimeric construct has been derived based on a high number of NMR observables including nuclear overhauser effects (NOEs), J-coupling constants and residual dipolar couplings (RDCs), which were all obtained with isotopically unlabeled molecules. Two 21-nt siRNA that efficiently hybridize consist of ribose units that were alternately substituted by 2′-fluoro or 2′-methoxy groups. Structure calculations utilized a set of H-F RDC values for all 21 2′-fluoro modified nucleotides under conditions of weak alignment achieved by Pf1 phages. A completely 2′-F/2′-OMe modified dimeric RNA construct adopts an antiparallel double-helical structure consisting of 19 Watson–Crick base pairs with additional 3′ UU overhangs and a 5′ phosphate group on the antisense strand. NMR data suggest that the stability of individual base pairs is not uniform throughout the construct. While most of the double helical segment exhibits well dispersed imino resonances, the last three base pairs either display uncharacteristic chemical shifts of imino protons or absence of imino resonances even at lower temperatures. Accessibility of imino protons to solvent exchange suggests a difference in stability of duplex ends, which might be of importance for incorporation of the guide siRNA strand into a RISC. |
format | Text |
id | pubmed-2978378 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-29783782010-11-12 Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct Podbevsek, Peter Allerson, Charles R. Bhat, Balkrishen Plavec, Janez Nucleic Acids Res Structural Biology A high-resolution solution structure of a stable 42-nt RNA dimeric construct has been derived based on a high number of NMR observables including nuclear overhauser effects (NOEs), J-coupling constants and residual dipolar couplings (RDCs), which were all obtained with isotopically unlabeled molecules. Two 21-nt siRNA that efficiently hybridize consist of ribose units that were alternately substituted by 2′-fluoro or 2′-methoxy groups. Structure calculations utilized a set of H-F RDC values for all 21 2′-fluoro modified nucleotides under conditions of weak alignment achieved by Pf1 phages. A completely 2′-F/2′-OMe modified dimeric RNA construct adopts an antiparallel double-helical structure consisting of 19 Watson–Crick base pairs with additional 3′ UU overhangs and a 5′ phosphate group on the antisense strand. NMR data suggest that the stability of individual base pairs is not uniform throughout the construct. While most of the double helical segment exhibits well dispersed imino resonances, the last three base pairs either display uncharacteristic chemical shifts of imino protons or absence of imino resonances even at lower temperatures. Accessibility of imino protons to solvent exchange suggests a difference in stability of duplex ends, which might be of importance for incorporation of the guide siRNA strand into a RISC. Oxford University Press 2010-11 2010-07-12 /pmc/articles/PMC2978378/ /pubmed/20624819 http://dx.doi.org/10.1093/nar/gkq621 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Structural Biology Podbevsek, Peter Allerson, Charles R. Bhat, Balkrishen Plavec, Janez Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct |
title | Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct |
title_full | Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct |
title_fullStr | Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct |
title_full_unstemmed | Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct |
title_short | Solution-state structure of a fully alternately 2′-F/2′-OMe modified 42-nt dimeric siRNA construct |
title_sort | solution-state structure of a fully alternately 2′-f/2′-ome modified 42-nt dimeric sirna construct |
topic | Structural Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978378/ https://www.ncbi.nlm.nih.gov/pubmed/20624819 http://dx.doi.org/10.1093/nar/gkq621 |
work_keys_str_mv | AT podbevsekpeter solutionstatestructureofafullyalternately2f2omemodified42ntdimericsirnaconstruct AT allersoncharlesr solutionstatestructureofafullyalternately2f2omemodified42ntdimericsirnaconstruct AT bhatbalkrishen solutionstatestructureofafullyalternately2f2omemodified42ntdimericsirnaconstruct AT plavecjanez solutionstatestructureofafullyalternately2f2omemodified42ntdimericsirnaconstruct |