PARALLEL DOUBLE-STRANDED HELICES AND THE TERTIARY STRUCTURE OF NUCLEIC-ACIDS

Thermal denaturation of four oligonucleotides, viz. 3'-d(AT)5pO(CH2)6Opd(AT)5-3' (par(AT)), 3'-d(AT)5pO(CH2)6Opd(AT)5-5'(anti(AT)),3'-d(A)10pO(CH2)6Op(T)10-3' (par(A-T)), and 3'-d(A)10pO(CH2)6Opd(T)10-5'(anti(A-T)), was studied in 0.01 M phosphate buffer, pH7, in the presence of 0.1, 0.25, 0.5 and 1.0 M NaCl. All the oligomers were found to exist at a lower temperature (0 to 20-degrees-C) as complexes composed either of two oligomer molecules (a canonical duplex) or of more oligomer molecules whereas, at a higher temperature (30 to 70-degrees-C), they formed hairpins with a parallel (par(AT) and par(A-T)) or antiparallel (anti(AT) and anti(A-T)) orientation of the chains. Melting curves (A260(T)) were used to calculate thermodynamic parameters for the formation of hairpins and "low-temperature" duplexes. Experiments on ethidium bromide binding to the oligonucleotides have shown that the oligomer anti(A-T) exists, at a low ionic strength, as a four stranded complex ("quadruplex") contains two antiparallel helices, d(A). d(T), which have a parallel orientation and are bound to one another owing to the formation of additional hydrogen bonds between nucleic acid bases. The possible biological function of quadruplexes is discussed.