Helix-Coil Transition of Parallel-Stranded DNA. Thermodynamics of Hairpin and Linear Duplex Oligonucleotides

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*T), stems (n = 8 or 10) and either a 5'-p-5' linkage in a d(C), loop (ps-C8 and ps-C10) or a 3'-p-3 ' linkage in a d(G), loop (ps-G10). The linear duplexes had 21-nt (ps-C2C3) and 25-nt (ps-DloD2, ps-D3.D4) mixed A,T sequences and normal chemical linkages throughout. Reference molecules with normal antiparallel helical orientations (hairpins aps-C8, aps-C 10, and aps-G10 and duplexes aps-C3-C7, aps-D 1.D3, and aps-D2.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 coun-terparts. 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 a t 252 nm, an isosbestic point at 267 nm, and a negative peak a t 282 nm. Temperature-dependent absorbances were recorded a t selected wavelengths and in the form of complete spectra to derive the thermodynamic parameters for the helix-coil transitions. The relativ