Kinetic analysis of the annealing period in the formation of the Poly (A)-2Poly (U) triple helix.

Synopsis The slow kinetics of annealing processes in multistranded nucleic acids is spectrophoto-metrically investigated using poly(A)-2poly(U) as a model system. The absorbance changes a t specific wavelengths show that double-helical (A-U) base pairs appear as transient inter-mediates. The annealing process is identified by the enlargement of triple-helical sequences a t the cost of (A-U) base pairs and unpaired (U) residues. A large time range in the reorganization of mismatched chain configurations is characterized by a logarithmic dependence on time. This observation is quantitatively described by a kinetic model developed by Jackson. In Jackson's model the rate-limiting process in the slow annealing phase of maximizing triple-helical sequences, is the removal of strand entanglements, knots, and hairpin loops by complete unwinding of those helical stretches which stabilize the mismatched configurations. The results of the present study are briefly discussed in terms of optimum conditions for hybridization experiments and for the preparation of polynucleotide complexes commonly used to produce interferons.