Title: Structural and Binding Study of Modified siRNAs with the Argonaute 2 PAZ Domain by NMR Spectroscopy
Authors: Maiti, Mohitosh ×
Nauwelaerts, Koen
Lescrinier, Eveline
Herdewijn, Piet #
Issue Date: Feb-2011
Publisher: VCH Verlagsgesellschaft
Series Title: Chemistry - a European Journal vol:17 issue:5 pages:1519-1528
Article number: 10.1002/chem.201000765
Abstract: By using high-resolution NMR spectroscopy, the structures of a natural short interfering RNA (siRNA) and of several altritol nucleic acid (ANA)-modified siRNAs were determined. The interaction of modified siRNAs with the PAZ domain of the Argonaute 2 protein of Drosophila melanogaster was also studied. The structures show that the modified siRNA duplexes (ANA/RNA) adopt a geometry very similar to the naturally occurring A-type siRNA duplex. All ribose residues, except for the 3' overhang, show 3'-endo conformation. The six-membered altritol sugar in ANA occurs in a chair conformation with the nucleobase in an axial position. In all siRNA duplexes, two overhanging nucleotides at the 3' end enhance the stability of the first neighboring base pair by a stacking interaction. The first overhanging nucleotide has a rather fixed position, whereas the second overhanging nucleotide shows larger flexibility. NMR binding studies of the PAZ domain with ANA-modified siRNAs demonstrate that modifications in the double-stranded region of the antisense strand have some small effects on the binding affinity as compared with the unmodified siRNA. Modification of the 3' overhang with thymidine (dTdT) residues shows a sixfold increase in the binding affinity compared with the unmodified siRNA (relative binding affinity of 17 % compared with dTdT-modified overhang), whereas modification of the 3' overhang with ANA largely decreases the binding affinity.
ISSN: 0947-6539
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Medicinal Chemistry (Rega Institute)
× corresponding author
# (joint) last author

Files in This Item:
File Description Status SizeFormat
2011026.pdf Published 850KbAdobe PDFView/Open Request a copy

These files are only available to some KU Leuven Association staff members


All items in Lirias are protected by copyright, with all rights reserved.

© Web of science