FREE-ENERGY OF THE BINDING OF URIDYLIC ACID OLIGOMERS WITH DOUBLE-STRANDED POLY(A)CENTER-DOT-POLY(U)

The binding parameters (K, omega) and the free energy (Delta G(0)) of triple helix formation have been estimated for complexes of oligo(U)(n ) (n = 5, 7-10) with poly(A) . poly(U) on the basis of hypochromicity measurements. The data were treated according to the formula of McGhee and von Hippel [J. Mol. Biol. 86 (1974) 469] by a computer program AL AU [H. Schutz et al., Stud. Biophys. 104 (1984) 23] which takes absorb ancies and total concentrations as input. In 1 mM cacodylate buffer pH 7.0 with 10 mM NaCl and 10 mM MgCl2 at 5 degrees C the free energy of contiguous binding was found to be a linear function of the oligomer length with a slope of Delta G(c,U)(0) = -0.72 (+/-0.03) kcal . mol(-1 ) per nucleotide. The mean cooperativity coefficient (omega) was 24.5 (+/-5.6), and the corresponding free energy of interaction between the neighbouring oligonucleotides in the third strand was Delta C-0 omega = -1.74 (+/-0.13) kcal . mol(-1). (C) 1997 Elsevier Science B.V.