4O41

Amide linked RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs.

Mutisya, D.Selvam, C.Lunstad, B.D.Pallan, P.S.Haas, A.Leake, D.Egli, M.Rozners, E.

(2014) Nucleic Acids Res. 42: 6542-6551

  • DOI: 10.1093/nar/gku235

  • PubMed Abstract: 
  • RNA interference (RNAi) has become an important tool in functional genomics and has an intriguing therapeutic potential. However, the current design of short interfering RNAs (siRNAs) is not optimal for in vivo applications. Non-ionic phosphate backb ...

    RNA interference (RNAi) has become an important tool in functional genomics and has an intriguing therapeutic potential. However, the current design of short interfering RNAs (siRNAs) is not optimal for in vivo applications. Non-ionic phosphate backbone modifications may have the potential to improve the properties of siRNAs, but are little explored in RNAi technologies. Using X-ray crystallography and RNAi activity assays, the present study demonstrates that 3'-CH2-CO-NH-5' amides are excellent replacements for phosphodiester internucleoside linkages in RNA. The crystal structure shows that amide-modified RNA forms a typical A-form duplex. The amide carbonyl group points into the major groove and assumes an orientation that is similar to the P-OP2 bond in the phosphate linkage. Amide linkages are well hydrated by tandem waters linking the carbonyl group and adjacent phosphate oxygens. Amides are tolerated at internal positions of both the guide and passenger strand of siRNAs and may increase the silencing activity when placed near the 5'-end of the passenger strand. As a result, an siRNA containing eight amide linkages is more active than the unmodified control. The results suggest that RNAi may tolerate even more extensive amide modification, which may be useful for optimization of siRNAs for in vivo applications.


    Organizational Affiliation

    Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
AMIDE LINKED RNAA,B,C,D12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SR
Query on SR

Download SDF File 
Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
URU
Query on URU
A, B, C, D
RNA LINKINGC20 H26 N5 O14 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.147 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 22.360α = 110.03
b = 34.330β = 94.24
c = 43.300γ = 95.83
Software Package:
Software NamePurpose
Singlephasing
MD2data collection
Singlemodel building
XSCALEdata scaling
MD2data collection
XDSdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-12-18 
  • Released Date: 2014-07-09 
  • Deposition Author(s): Pallan, P.S., Egli, M.

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Refinement description