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Free energy of the binding of uridylic acid oligomers with double stranded poly cntdotpoly


, : Free energy of the binding of uridylic acid oligomers with double stranded poly cntdotpoly. Biophysical Chemistry 67(1-3): 245-261, Sept 1

The binding parameters (K, omega) and the free energy (DELTAG0) of triple helix formation have been estimated for complexes of oligo(U)n (n = 5, 7-10) with poly(A) cntdot 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) 4691 by a computer program ALAU (H. Schutz et al., Stud. Biophys. 104 (1984) 231 which takes absorbancies and total concentrations as input. In 1 mM cacodylate buffer pH 7.0 with 10 mM NaCl and 10 mM MgCl2 at 5degreeC the free energy of contiguous binding was found to be a linear function of the oligomer length with a slope of DELTAGc.U0 = -0.72 (+-0.03) kcal cntdot 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 DELTAG0omega = -1.74 (+-0.13) kcal cntdot mol-1.

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