1JVE image
Deposition Date 2001-08-29
Release Date 2002-05-22
Last Version Date 2024-05-22
Entry Detail
PDB ID:
1JVE
Keywords:
Title:
NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop
Biological Source:
Source Organism:
(Taxon ID: )
Method Details:
Experimental Method:
Conformers Calculated:
50
Conformers Submitted:
10
Selection Criteria:
Lowest target function (a weighted sum of conformational energy and restraint energy).
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:AT-Rich DNA with the GAA-Hairpin Loop
Chain IDs:A
Chain Length:27
Number of Molecules:1
Biological Source:
Primary Citation
High-resolution NMR structure of an AT-rich DNA sequence.
J.Biomol.NMR 22 265 280 (2002)
PMID: 11991355 DOI: 10.1023/A:1014987532546

Abstact

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.

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