1AO9

INTRAMOLECULAR DNA DUPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GAGAGA-X-TCTCCT), NMR, 12 STRUCTURES

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 1997-07-22 Released: 1998-01-28 
  • Deposition Author(s): Bartley, J.P.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 12 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex.

Bartley, J.P.Brown, T.Lane, A.N.

(1997) Biochemistry 36: 14502-14511

  • DOI: 10.1021/bi970710q
  • Primary Citation of Related Structures:  
    1AO9, 1AT4

  • PubMed Abstract: 
  • The solution properties of the parallel intramolecular DNA triplex d(GAGAGA-oct-TCTCTC-oct-CTCTCT) (oct = -O-(CH2)8-O-PO2-O-(CH2)8-O-PO2-) and the duplex d(GAGAGA-oct-TCTCTC) have been examined by UV melting and high-resolution nuclear magnetic resonance spectroscopy (NMR) ...

    The solution properties of the parallel intramolecular DNA triplex d(GAGAGA-oct-TCTCTC-oct-CTCTCT) (oct = -O-(CH2)8-O-PO2-O-(CH2)8-O-PO2-) and the duplex d(GAGAGA-oct-TCTCTC) have been examined by UV melting and high-resolution nuclear magnetic resonance spectroscopy (NMR). All nucleotides were primarily in the S conformation (i.e. near C2'-endo) in both the duplex and the triplex. However, the sugars of the Hoogsteen pyrimidine strand had a lower fraction of the S state than the Watson-Crick strands. Glycosidic torsion angles derived from nuclear Overhauser effect (NOE) build-up curves were found in the range -103 degrees to -133 degrees, with a clear alternation in magnitude along the GAGAGA strand in the triplex, whereas the glycosidic torsion angles were more similar in the duplex. Internucleotide NOEs were also consistent with an overall B-like geometry, rather than the A family. However, particularly in the Hoogsteen strand, some sequential NOE intensities were intermediate between those of the B and A forms. Distance and torsion constraints derived from NMR experiments were used to generate structures and were refined by restrained molecular dynamics. Extensive chemical shift differences between residues in the triplex and duplex were found for the purine strand, and there were remarkable differences in the pattern of shift differences for the A and G residues that correlated with differences in glycosidic torsion angles. Although there are differences in structure between the free duplex and that in the triplex, they are in important respects similar, indicating that only small conformational adjustments are needed to make parallel triple helices.


    Organizational Affiliation

    Department of Chemistry, Queensland University of Technology, Brisbane, Australia.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*C)-3')A13N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 12 
    • Conformers Submitted: 12 
    • Selection Criteria: LEAST RESTRAINT VIOLATION 
    • OLDERADO: 1AO9 Olderado

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    • Deposited Date: 1997-07-22 
    • Released Date: 1998-01-28 
    • Deposition Author(s): Bartley, J.P.

    Revision History  (Full details and data files)

    • Version 1.0: 1998-01-28
      Type: Initial release
    • Version 1.1: 2008-03-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance