1JVE

NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: Lowest target function (a weighted sum of conformational energy and restraint energy). 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution NMR structure of an AT-rich DNA sequence.

Ulyanov, N.B.Bauer, W.R.James, T.L.

(2002) J.Biomol.NMR 22: 265-280


  • PubMed Abstract: 
  • We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTATAA x TTATAATTA, is imbedded in a 27-nucle ...

    We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTATAA x TTATAATTA, is imbedded in a 27-nucleotide stem-and-loop construct, which is stabilized by terminal GC base pairs and an extraordinarily stable DNA loop GAA (Hirao et al., 1994, Nucleic Acids Res. 22, 576-582). The AT-rich sequence has three repeated TAA x TTA motifs, one in the reverse orientation. Comparison of the local conformations of the three motifs shows that the sequence context has a minor effect here: atomic RMSD between the three TAA x TTA fragments is 0.4-0.5 A, while each fragment is defined within the RMSD of 0.3-0.4 A. The AT-rich stem also contains a consensus sequence for the Pribnow box, TATAAT. The TpA, ApT, and TpT x ApA steps have characteristic local conformations, a combination of which determines a unique sequence-dependent pattern of minor groove width variation. All three TpA steps are locally bent in the direction compressing the major groove of DNA. These bends, however, compensate each other, because of their relative position in the sequence, so that the overall helical axis is essentially straight.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
AT-Rich DNA with the GAA-Hairpin LoopA27N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 10 
  • Selection Criteria: Lowest target function (a weighted sum of conformational energy and restraint energy). 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance