1R3G

1.16A X-ray structure of the synthetic DNA fragment with the incorporated 2'-O-[(2-Guanidinium)ethyl]-5-methyluridine residues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

2'-O-[2-(Guanidinium)ethyl]-Modified Oligonucleotides: Stabilizing Effect on Duplex and Triplex Structures.

Prakash, T.P.Lesnik, E.Mohan, V.Tereshko, V.Egli, M.Manoharan, M.

(2004) Org Lett 6: 1971-1974

  • DOI: https://doi.org/10.1021/ol049470e
  • Primary Citation of Related Structures:  
    1R3G

  • PubMed Abstract: 

    [structure: see text] Oligonucleotides with a novel 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modification have been synthesized using a novel protecting group strategy for the guanidinium group. This modification enhances the binding affinity of oligonucleotides to RNA as well as duplex DNA (DeltaT(m) 3.2 degrees C per modification). The 2'-O-GE modified oligonucleotides exhibited exceptional resistance to nuclease degradation. The crystal structure of a palindromic duplex formed by a DNA oligonucleotide with a single 2'-O-GE modification was solved at 1.16 A resolution.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*GP*TP*AP*(GMU)P*AP*CP*GP*C)-3')
A, B
10N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.111α = 90
b = 43.151β = 90
c = 45.558γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-21
    Type: Initial release
  • Version 1.1: 2008-01-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations