1R3G

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

• PDB DOI: https://doi.org/10.2210/pdb1R3G/pdb
• NAKB: 1R3G

• Classification: DNA
• Mutation(s): No 


• Deposited: 2003-10-01 Released: 2003-10-21 
• Deposition Author(s): Prakash, T.P., Puschl, A., Lesnik, E., Tereshko, V., Egli, M., Manoharan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

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

• PubMed: 15176796 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.32 kDa 
• Atom Count: 575 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*AP*(GMU)P*AP*CP*GP*C)-3')	A, B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	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 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.111	α = 90
b = 43.151	β = 90
c = 45.558	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-21 
Deposition Author(s): Prakash, T.P., Puschl, A., Lesnik, E., Tereshko, V., Egli, M., Manoharan, M.

Revision History  

• 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