Journal
JOURNAL OF BIOMOLECULAR NMR
Volume 22, Issue 3, Pages 265-280Publisher
SPRINGER
DOI: 10.1023/A:1014987532546
Keywords
AT-rich sequence; DNA; GAA loop; NMR; Pribnow box; stem-and-loop structure
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Funding
- NATIONAL CENTER FOR RESEARCH RESOURCES [P41RR001081] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM039247] Funding Source: NIH RePORTER
- NCRR NIH HHS [P41 RR01081] Funding Source: Medline
- NIGMS NIH HHS [GM39247] Funding Source: Medline
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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.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.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.TTA fragments is 0.4-0.5 Angstrom, while each fragment is defined within the RMSD of 0.3-0.4 Angstrom. The AT-rich stem also contains a consensus sequence for the Pribnow box, TATAAT. The TpA, ApT, and TpT.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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