1P0U

Sheared G/C Base Pair


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 10 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sheared-type G(anti).C(syn) Base-pair: A Unique d(GXC) Loop Closure Motif.

Chin, K.H.Chou, S.H.

(2003) J.Mol.Biol. 329: 351-361


  • PubMed Abstract: 
  • Stable DNA loop structures closed by a novel G.C base-pair have been determined for the single-residue d(GXC) loops (X=A, T, G or C) in low-salt solution by high-resolution nuclear magnetic resonance (NMR) techniques. The closing G.C base-pair in the ...

    Stable DNA loop structures closed by a novel G.C base-pair have been determined for the single-residue d(GXC) loops (X=A, T, G or C) in low-salt solution by high-resolution nuclear magnetic resonance (NMR) techniques. The closing G.C base-pair in these loops is not of the canonical Watson-Crick type, but adopts instead a unique sheared-type (trans Watson-Crick/sugar-edge) pairing, like those occurring in the sheared mismatched G.A or A.C base-pair, to draw the two opposite strands together. The cytidine residue in the closing base-pair is transformed into the rare syn domain to form two H-bonds with the guanine base and to prevent the steric clash between the G 2NH(2) and the C H-5 protons. Besides, the sugar pucker of the syn cytidine is still located in the regular C2'-endo domain, unlike the C3'-endo domain adopted for the pyrimidines of the out-of-alternation left-handed Z-DNA structure. The facile formation of the compact d(GXC) loops closed by a unique sheared-type G(anti).C(syn) base-pair demonstrates the great potential of the single-stranded d(GXC) triplet repeats to fold into stable hairpins.


    Organizational Affiliation

    Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*AP*TP*CP*GP*AP*CP*GP*AP*TP*GP*C)-3'A13N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 10 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-04-11 
  • Released Date: 2003-06-03 
  • Deposition Author(s): Chin, K.H., Chou, S.H.

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance