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Title: Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gkx558· OSTI ID:1397293
 [1];  [2];  [1];  [3];  [4];  [3];  [2];  [2];  [1]
  1. Binghamton Univ., NY (United States)
  2. GE Healthcare Dharmacon, Lafayette, CO (United States)
  3. Vanderbilt Univ., Nashville, TN (United States)
  4. Univ. of Rochester, NY (United States)
+ Show Author Affiliations

While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA–DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)
Grant/Contract Number:
1S10 OD012254; CHE-0922815; R01 GM71461
OSTI ID:
1397293
Journal Information:
Nucleic Acids Research, Vol. 45, Issue 14; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 23 works
Citation information provided by
Web of Science

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Cited By (4)

Synthesis and Biological Activity of Short Interfering RNAs Having Several Consecutive Amide Internucleoside Linkages journal December 2019
Modeling of canonical and C2′- O -thiophenylmethyl modified hexamers of RNA. Insights into the nature of structural changes and thermal stability journal January 2018
Studies on sugar puckering and glycosidic stabilities of 3′-amino-5′-carboxymethyl-3′,5′-dideoxy nucleoside mimics journal January 2018
Current Development of siRNA Bioconjugates: From Research to the Clinic journal April 2019

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