Helix-coil transition of parallel-stranded DNA. Thermodynamics of hairpin and linear duplex oligonucleotides

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Abstract
The stabilities have been determined of different DNA double helices constructed with the two constituent strands in a parallel orientation. These molecules incorporate polarity-inverting loop structures (hairpins) or nucleotide sequences (duplexes) which impose the desired polarity on the two strands constituting the sugar-phosphate backbone. The hairpins consisted of d(A .cntdot. T)n stems (n = 8 or 10) and either a 5''-p-5'' linkage in a d(C)4 loop (ps-C8 and ps-C10) or a 3''-p-3'' linkage in a d(G)4 loop (ps-G10). The linear duplexes had 21-nt (ps-C2 .cntdot. C3) and 25-nt (ps-D1 .cntdot. D2, ps D3 .cntdot. D4) mixed A,T sequences and normal chemical linkages throughout. Reference molecules with normal antiparallel helical orientations (hairpins aps-C8, aps-C10, and aps-G10 and duplexes aps-C3 .cntdot. C7, aps-D1 .cntdot. D3, and aps-D2 .cntdot. D4) were also synthesized and studied. Hydrogen bonding in ps-DNA is via reverse Watson-Crick base pairs, and the various constructs display spectroscopic, chemical, biochemical, and electrophoretic properties distinct from those of their aps counterparts. For example, both the ps and aps molecules show a pronounced UV absorption hyperchromicity upon melting, but the spectral distribution is not the same. Thus, the difference spectra (ps - aps) in the native state are characterized by a positive peak at 252 nm, an isosbestic point at 267 nm, and a negative peak at 282 nm. Temperature-dependent absorbances were recorded at selected wavelengths and in the form of complete spectra to derive the thermodynamic parameters for the helix-coil transitions. The relative absorption changes as well as the thermodynamic parameters are in accordance with an intramolecular helix-coil transition for the hairpins and a bimolecular transition for the linear duplexes. There is no indication of higher order structures such as dimers and concatamers. The van''t Hoff melting enthalpies .DELTA.HvH are found to be independent of salt concentration and about 20% lower in the case of the ps-DNAs. The latter also exhibit lower melting temperatures, Tm, by about 10 and 15.degree. C for the hairpins and duplexes, respectively. However, all the DNAs show a similar dependency upon salt concentration (.vdelta.Tm/.vdelta. log [NaCl] = 17 .+-. 3.degree. C). Parallel-stranded DNA is second only to B-DNA in helical stability under physiological salt conditions and temperature.