1PQT

REFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BOND RESIDUAL DIPOLAR COUPLINGS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 14 
  • Conformers Submitted: 14 
  • Selection Criteria: all calculated structures submitted 

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This is version 1.2 of the entry. See complete history


Literature

Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-Bond Residual Dipolar Couplings

Padrta, P.Stefl, R.Kralik, L.Zidek, L.Sklenar, V.

(2002) J Biomol NMR 24: 1-14

  • DOI: 10.1023/a:1020632900961
  • Primary Citation of Related Structures:  
    1KR8, 1PQT

  • PubMed Abstract: 
  • The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints ...

    The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond 1H-13C, 1H-15N, 13C-13C and 13C-15N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.


    Organizational Affiliation

    National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*GP*AP*AP*GP*C)-3'A7N/A
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 14 
    • Conformers Submitted: 14 
    • Selection Criteria: all calculated structures submitted 
    • OLDERADO: 1PQT Olderado

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2003-07-01
      Type: Initial release
    • Version 1.1: 2008-04-29
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance