Cooperative interactions in single-strand oligomers of adenylic acid

✍ Scribed by Douglas Poland; John N. Vournakis; Harold A. Scheraga

• Publisher: Wiley (John Wiley & Sons)
• Year: 1966
• Tongue: English
• Weight: 680 KB
• Volume: 4
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.1966.360040209

✦ Synopsis

Optical rotatory dispersion measurements were made on the oligonucleotides (pA)s, (PA)+ and PA)^ at neutral pH over the temperature range 5-85"C., and compared to similar data for polyriboadenylic acid: The data were interpreted in terms of a temperature-dependent stacking of the bases in the singlestrand oligomers, with very little dependence of the degree of stacking on the chain length. These results can be explained by a theory of cooperative stacking. The degrees of freedom available per residue are rotations about the five backbone covalent bonds and the bond connecting the base to the ribose ring. To nucleate a stacking interaction between neighboring bases the backbone sequence must be ordered as must be the two bases. For this stack to grow by one base a backbone sequence must again be ordered, but only one additional base must be ordered. Thus, the degree of freedom of the base with respect to the ribose ring determines the extent of the cooperative effect and hence the effect of chain length. A matrix formulation of the partition function is presented which incorporates this cooperative nature of the interaction and is shown to be in fair agreement with the data. The entropy of ordering a base with respect to the ribose ring is found to be 0.68 e.u., which suggests that the purine has a torsional oscillation when unstacked, but does not have several koenergetic positions of internal rotation available. The enthalpy of stacking is found to be -6.5 kcal./mole. A model involving neighbor and next-nearest neighbor interactions could also account for the data. For all practical purposes, the stacking interactions of successive residues can be treated as independent, i.e., the state of one residue is essentially independent of the state of stacking of its neighbors.