1BCE

INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: ENERGY, NMR R FACTORS 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets.

Asensio, J.L.Brown, T.Lane, A.N.

(1998) Nucleic Acids Res 26: 3677-3686

  • DOI: 10.1093/nar/26.16.3677
  • Primary Citation of Related Structures:  
    1BCE, 1BCB

  • PubMed Abstract: 
  • The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds ...

    The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with >19 restraints per residue are very similar (RMSD = 0.96 A). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximately 60 degrees and gamma approximately 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.


    Related Citations: 
    • The Contribution of Cytosine Protonation to the Stability of Parallel DNA Triple Helices
      Asensio, J.L., Lane, A.N., Dhesi, J., Bergqvist, S., Brown, T.
      (1998) J Mol Biol 275: 811

    Organizational Affiliation

    Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*GP*GP*AP*A)-3')A6N/A
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    • Reference Sequence
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    • Entity ID: 2
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      DNA (5'-D(*TP*TP*CP*CP*TP*T)-3')B, C6N/A
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: SOLUTION NMR
      • Conformers Calculated: 50 
      • Conformers Submitted: 10 
      • Selection Criteria: ENERGY, NMR R FACTORS 
      • OLDERADO: 1BCE Olderado

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1998-08-12
        Type: Initial release
      • Version 1.1: 2008-03-24
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance