Complex formation between oligonucleotides and polymers.

Both deoxyribonucleic and ribonucleic acids appear to possess a secondary structure, by virtue of the fact that the purine and pyrimidine bases can undergo hydrogen bonding with each other. In the case of DNA, this secondary structure takes the form of a long, highly ordered helix composed of two strands held to each other by hydrogen bonds between the bases (l-3). The secondary structure of RNA is less regular, and Doty et al. (4) have suggested that it consists of small loops. These would be short stretches of two-stranded regions held together by fortuitous matching of complementary base pairs on the two strands, and separated by other short stretches that are unbonded. It is difficult to evaluate the relative bond stabilities of the different base pairs in DNA (adenine-thymine, guanine-cytosine) or RNA (adenine-uracil, guanine-cytosine) because they occur simultaneously within the same molecule, although an estimation of the contribution of guanine-cytosine pairing has been made (5). However, with synthetic homopolymers of nucleotides, it is possible to study directly the strengths of specific base pairs. In addition, it is now possible to assess the relative stabilities of small lengths of hydrogen-bonded helices, since the formation of helical complexes between long-chain polyribonucleotides and oligonucleotides has been described (6) .I The relative strengths of the component bonds in such complexes can be determined by measuring the thermal stability of the complexes, e.g. the temperature at which they are half-dissociated (T,) (4). In addition, the effects of alterations in the structure of the oligonucleotide component on the bond strength of the resulting complex can be measured. This paper is concerned with the changes in bond stability resulting from variations in the end groups, the number and type of bases, and the sugar in the oligonucleotide moiety of the complex.