Intramolecular interaction of thymine and adenine bases in synthetic oligo- and polynucleotide models.

Four types of oligomer systems, ranging from monomers to hexamers, of linear polyethyleneimine derivatives having pendant thymine or adenine bases were prepared. In order to evaluate the intramolecular interaction between the pendant nucleic acid bases, ultraviolet spectra at various pH regions and proton NMR spectra at various temperatures were measured. The results on UV hypochromicities and pKa values led to the clarification of such interaction between the bases: adenine bases can be prone to interact intramolecularly by stacking, while the interaction between thymine bases is not due to stacking, but due only to residual interaction which takes place between neighboring chromophores.