Characterization of a parallel-stranded DNA hairpin
- Univ. of Calgary, Alberta (Canada)
Recently, the authors have shown that synthetic DNA containing homooligomeric A-T base pairs can form a parallel-stranded intramolecular hairpin structure. In the present study, they have employed NMR and optical spectroscopy to investigate the structure of the parallel-stranded (PS) DNA hairpin 3{prime}-d(T){sub 8}C{sub 4}(A){sub 8}-3{prime} and the related antiparallel (APS) hair 5{prime}-d(T){sub 8}C{sub 4}(A){sub 8}-3{prime}. The parallel orientation of the strands in the PS oligonucleotide is achieved by introducing a 5{prime}-5{prime} phosphodiester linkage in the hairpin loop. Ultraviolet spectroscopic and fluorescence data of drug binding are consistent with the formation of PS and APS structures, respectively, in these two hairpins. Vacuum circular dichroism measurements in combination with theoretical CD calculations indicate that the PS structure forms a right-handed helix. {sup 31}P NMR measurements indicate that the conformation of the phosphodiester backbone of the PS structure is not drastically different from that of the APS control. The presence of slowly exchanging imino protons at 14 ppm and the observation of nuclear Overhauser enhancement between imino protons and the AH-2 protons demonstrate that similar base pairing and base stacking between T and A residues occur in both hairpins. On the basis of NOESY measurements, they find that the orientation of the bases is in the anti region and that the sugar puckering is in the 2{prime}-endo range. The results indicate a B-like conformation for each of the strands in the stem part of the PS hairpin and reverse Watson-Crick base pairing between the T and A residues. These data are consistent with a previously calculated structure for parallel-stranded DNA.
- OSTI ID:
- 5442455
- Journal Information:
- Biochemistry; (USA), Vol. 28:15; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
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550601* - Medicine- Unsealed Radionuclides in Diagnostics