1X2S

NMR solution structures of a DNA dodecamer containing a tandem GT mismatches using NOE and residual dipolar couplings


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

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Literature

NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G--T mismatches

Alvarez-Salgado, F.Desvaux, H.Boulard, Y.

(2006) Magn Reson Chem 44: 1081-1089

  • DOI: 10.1002/mrc.1902
  • Primary Citation of Related Structures:  
    1X2O, 1X30, 1X2Z, 1X2Y, 1X2X, 1X2V, 1X2U, 1X2S

  • PubMed Abstract: 
  • We have carried out a solution study of two non-labelled self-complementary DNA dodecamers d(GACTGTACAGTC)2 and d(GACTGTGCAGTC)2 by NMR, the second sequence composed of two G-T mismatches. Structures were determined using distances extracted from NOE effects alone or using both NOE and RDC constraints, measured in three different liquid crystalline media ...

    We have carried out a solution study of two non-labelled self-complementary DNA dodecamers d(GACTGTACAGTC)2 and d(GACTGTGCAGTC)2 by NMR, the second sequence composed of two G-T mismatches. Structures were determined using distances extracted from NOE effects alone or using both NOE and RDC constraints, measured in three different liquid crystalline media. We ensured that our data on the influence of the mesogen on the DNA structures, and the way in which the RDCs were incorporated as constraints in the protocol refinement, were consistent. We also tested the influence of different sets of RDCs and the best means of optimizing the calculation of D(a) and R. Resolution and accuracy of the ten best energy final structures were compared. The addition of a small set of RDC constraints significantly improves the final determined structures. We took advantage of the specificity of the RDC, i.e. it contains orientational information, and explored the global shape of the DNA duplexes; it was found that the duplexes do not have a large curvature. For the G-T base pair, we observed, in this particular sequence (tandem of G-T mismatches), a new pattern of base pairing, which involved the formation of a bifurcated hydrogen bond.


    Organizational Affiliation

    Laboratoire du Contrôle du Cycle Cellulaire, DSV/DBJC, Service de Biochimie et de Génétique Moléculaire, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*AP*CP*TP*GP*TP*AP*CP*AP*GP*TP*C)-3'A, B12N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Submitted: 
    • OLDERADO: 1X2S Olderado

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2006-08-01
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance