8PSH

HIGH RESOLUTION NMR STRUCTURE OF THE STEREOREGULAR (ALL-RP)-PHOSPHOROTHIOATE-DNA/RNA HYBRID D (G*PS*C*PS*G*PS*T*PS*C*PS*A*PS*G*PS*G)R(CCUGACGC), MINIMIZED AVERAGE STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb8PSH/pdb
• NAKB: 8PSH

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


• Deposited: 1997-10-13 Released: 1998-05-27 
• Deposition Author(s): Bachelin, M., Hessler, G., Kurz, G., Hacia, J.G., Dervan, P.B., Kessler, H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 1 
• Selection Criteria: AVERAGE OF ALL STRUCTURES 

Literature

Structure of a Stereoregular Phosphorothioate DNA/RNA Duplex

Bachelin, M., Hessler, G., Kurz, G., Hacia, J.G., Dervan, P.B., Kessler, H.

(1998) Nat Struct Biol 5: 271-276

• PubMed: 9546216 
• DOI: https://doi.org/10.1038/nsb0498-271
• Primary Citation of Related Structures:  
  8DRH, 8PSH


• PubMed Abstract: 
  

  In this work, we present the first NMR solution structure of a DNA/RNA hybrid containing stereoregular Rp-phosphorothioate modifications of all DNA backbone linkages. The complex of the enzymatically synthesized phosphorothioate DNA octamer (all-Rp)-d(GCGTCAGG) and its complementary RNA r(CCUGACGC) was found to adopt an overall conformation within the A-form family. Most helical parameters and the sugar puckers of the DNA strand assume values intermediate between A- and B-form. The close structural similarity with the unmodified DNA/RNA hybrid of the same sequence may explain why both the natural and the sulfur-substituted complex can be recognized and digested by ribonuclease H.

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Organizational Affiliation: 

Institut für Organische Chemie und Biochemie, TU München, Garching, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.08 kDa 
• Atom Count: 329 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DGP*(SC)P*(GS)P*(PST)P*(SC)P*(AS)P*(GS)P*(GS))-3')	A	8	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*CP*UP*GP*AP*CP*GP*C)-3')	B	8	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 1 
• Selection Criteria: AVERAGE OF ALL STRUCTURES 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-27 
Deposition Author(s): Bachelin, M., Hessler, G., Kurz, G., Hacia, J.G., Dervan, P.B., Kessler, H.

Revision History  

• Version 1.0: 1998-05-27
  Type: Initial release
  
• Version 1.1: 2008-03-20
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-16
  Changes: Data collection, Database references, Derived calculations, Other