168D

STABILIZING EFFECTS OF THE RNA 2'-SUBSTITUENT: CRYSTAL STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE DUPLEX CONTAINING 2'-O-METHYLATED ADENOSINES

• PDB DOI: https://doi.org/10.2210/pdb168D/pdb
• NAKB: 168D

• Classification: DNA-RNA HYBRID
• Mutation(s): No 


• Deposited: 1994-04-08 Released: 1994-08-31 
• Deposition Author(s): Lubini, P., Zuercher, W., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.193 

Literature

Stabilizing effects of the RNA 2'-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2'-O-methylated adenosines.

Lubini, P., Zurcher, W., Egli, M.

(1994) Chem Biol 1: 39-45

• PubMed: 9383369 
• DOI: https://doi.org/10.1016/1074-5521(94)90039-6
• Primary Citation of Related Structures:  
  168D


• PubMed Abstract: 
  

  The stability of hybrids of 2'-O-methyl-ribonucleotides with complementary RNA is considerably higher than that of the corresponding DNA.RNA duplexes. The 2'-O-modified ribonucleotides are thus an attractive class of compounds for antisense applications. Understanding how these substituents stabilize the structure of the hybrid duplex may be important in the design of ribonucleotides with novel properties.

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Organizational Affiliation: 

Organic Chemistry Laboratory, ETH Swiss Federal Institute of Technology, Zürich, Switzerland.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.15 kDa 
• Atom Count: 461 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-D(*GP*CP*GP*TP*)-R(*(A2M)P*)-D(*TP*AP*CP*GP*C)-3')	A, B	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.13	α = 90
b = 45.649	β = 90
c = 47.554	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement
MODIFIED	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-08-31 
Deposition Author(s): Lubini, P., Zuercher, W., Egli, M.

Revision History  

• Version 1.0: 1994-08-31
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Structure summary