Characterization of a parallel stranded DNA hairpin

Abstract

Recently we have shown that synthetic DNA containing homooligomeric A-T base pairs can form a parallel-stranded intramolecular hairpin structure [van de Sande et al. (1988) Science (Washington, D.C.) 241, 551-557]. In the present study, we have employed NMR and optical spectroscopy to investigate the structure of the parallel-stranded (PS) DNA hairpin 3'-d(T)8C4(A)8-3' and the related antiparallel (APS) hairpin 5'-d(T)8C4(A)8-3'. The parallel orientation of the strands in the PS oligonucleotide is achieved by introducing a 5'-5' 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. 31P 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. However, the small chemical shift dispersion observed in proton NMR spectra of the PS hairpin suggests that the stem of this hairpin is more regular than that of the APS hairpin. On the basis of NOESY measurements, we find that the orientation of the bases is in the anti region and that the sugar puckering is in the 2'-endo range.(ABSTRACT TRUNCATED AT 250 WORDS)

Parallel-stranded DNA with Hoogsteen base pairing stabilized by a trans-[Pt(NH3)2]2+ cross-link: characterization and conversion into a homodimer and a triplex

“…Upon formation of the cross-link the melting temperature of the duplex increases from 21 C to 35 C (pH 4.2). Interestingly, the thermodynamic melting data determined for psPt at pH 4.2 are in good agreement with those for the ps hairpin structure of 39-d(T 8 *C 4 A 8 )-39 (*=59-59 linkage) which at pH 6.5 consists of rWC base pairs (T m =35.2 C, DH vH =154 kJ mol ±1 , DS=500 J mol ±1 K ±1 ) [25]. In that work, a cytosine loop was used to covalently attach the two parallel strands to one another.…”

“…Despite the fact that the NMR spectra of psPt cannot be completely assigned owing to a severe overlap of signals, which is more serious than with aps DNA because of the higher symmetry of ps DNA [25], some important conclusions on the conformation of the cross-linked nucleobases can be drawn from the NOESY spectra. The H8 signals of the two platinated guanines can easily be identified on the basis of their characteristic low-field shift that occurs upon metalation [27].…”

Dynamics and relative stabilities of parallel- and antiparallel-stranded DNA duplexes

“…The melting temperature of ps-DNA are 13-19°C lower than for similar aps-DNA sequences (German, 1988;Ramsing, 1988; Rippe, 1989a, b;Rentzeperis, 1992). 1H NMR and 31P NMR studies (Germann, 1989) show that ps-DNA exhibit large backbone flexibility. A large number of P NMR resonances suggest that many E and , dihedral angles can be sampled by the backbone (Powers, 1989(Powers, , 1990 Lankhorst, 1984).…”

Distamycin-stabilized Antiparallel-Parallel Combination (APC) DNA

“…The existence of stable DNA duplexes with strands oriented parallel to each other is well documented (1)(2)(3)(4)(5)(6) and leads immediately to a consideration of mechanisms by which this conformation can arise from B-DNA. General schemes for such interconversions have been presented in numerous publications (2,3,(7)(8)(9)(10).…”