The poly(dT).2poly(dA) triple helix.

Abstract

A new homopolynucleotide triple helix, (dT)n.2(dA)n, detected by circular dichroism mixing curves, is the product of an endothermic reaction of (dA)n.(dT)n with (dA)n at moderate temperatures and high salt concentrations ([NaCl] > or = 2.6 M): (dA)n.(dT)n + (dA)n<-->(dT)n.2(dA)n. At higher temperatures (dT)n.2(DA)n forms from the (dA)n.(dT)n duplex alone: 3[(dA)n.(dT)n]<-->(dT)n.2(dA)n + (dA)n.2(dT)n. Upon further heating, (dT)n.2(dA)n is converted to the triplex (dA)n.2(dT)n: 2[(dT)n.2(dA)n]<-->(dA)n.2(dT)n + 3(dA)n. (dT)n.2(dA)n forms owing to a favorable entropy change; delta Hm is unfavorable, ranging from 1 to 2.5 kcal mol-1, depending upon [NaCl]. The formation reaction is associated with a negative change in heat capacity. (dT)n.2(dA)n is an extremely weak complex with a free energy of stabilization, delta Go < or = 100 cal mol-1. Tm values of ultraviolet, circular dichroism, and differential scanning calorimetry transition curves for the formation of (dT)n.2(dA)n decrease with increasing [NaCl], reflecting, in part, the net uptake of cations. The values of (dTm/d ln a +/- )(delta Hm/RTm2) can be accounted for in terms of the charge spacing and cylindrical dimensions of the polynucleotides. The ionic strength dependence of this quantity is consistent with interaction of anions with (dAn). High concentrations of the anions Cl-, Br-, and ClO4- decrease the stability of (dT)n.2(dA)n according to the lyotropic series. The highly polarizable anion, ClO4-, entirely prevents the formation of (dT)n.2(dA)n. Phase diagrams of the (dA)n,(dT)n system in solutions of NaCl, NaBr, and NaClO4 are presented. A bonding scheme for (dT)n.2(dA)n is proposed, and implications of this work for Py.Pu.Pu triple helices are discussed.