Transition characteristics and thermodynamic analysis of DNA duplex formation: a quantitative consideration for the extent of duplex association

Transition characteristics and thermodynamic properties of the single-stran ded self-transition and the double-stranded association were investigated a nd analyzed for 9-, 15- and 21-bp non-self-complementary DNA sequences. The multiple transition processes for the single-stranded self-transition and the double-stranded association were further put forth. The experimental re sults confirmed that the double-stranded association transition was general ly imperfect and the thermodynamic properties of the single-stranded self-t ransition would exert an influence on a duplex formation. Combining ultravi olet melting experiments in various molar ratios, the extent of duplex asso ciation was estimated for three double-stranded DNAs. In our experimental r ange, the extent of duplex association decreases with increasing the number of base pairs in DNA sequences, which suggest that the short oligonucleoti des may proceed in a two-state transition while the long oligonucleotides m ay not. When the extent of duplex association was considered, the true tran sition enthalpies of a duplex formation derived from UV and differential sc anning calorimetry measurements were in good agreement.