Macromolecule Content

• Total Structure Weight: 6820.58 
• Atom Count: 448 
• Residue Count: 24 
• Unique nucleic acid chains: 1

225D

A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS

• DOI: 10.2210/pdb225D/pdb
• NDB: 225D

• Classification: DNA


• Deposited: 1995-07-12 Released: 1995-10-15 
• Deposition Author(s): Gehring, K., Leroy, J.L., Gueron, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

A tetrameric DNA structure with protonated cytosine.cytosine base pairs.

Gehring, K., Leroy, J.L., Gueron, M.

(1993) Nature 363: 561-565

• PubMed: 8389423 
• DOI: 10.1038/363561a0


• PubMed Abstract: 
  

Oligomers containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5'-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and constrained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs H1'-H1', H1'-H2" and H1'-H4'. These NOEs are probably diagnostic for such tetrameric structures.

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Organizational Affiliation: 

Groupe de Biophysique de l'Ecole Polytechnique et de l'URA D1254 du CNRS, Palaiseau, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*TP*CP*CP*CP*CP*C)-3')	A,B,C,D	6	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-07-12 
• Released Date: 1995-10-15 
• Deposition Author(s): Gehring, K., Leroy, J.L., Gueron, M.

Revision History 

• Version 1.0: 1995-10-15
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance