On the application of polyelectrolyte limiting laws to the helix-coil transition of DNA. V. Ionic effects on renaturation kinetics.

Abstract

AbstractThe bimolecular rate constant k2 for the association of complementary polynucleotide strands has been observed to increase strongly with increasing ionic strength—in fact, proportional to its third or fourth power. This effect is here interpreted quantitatively by means of polyelectrolyte theory starting with the Wetmur–Davidson postulate of a pre‐equilibrium between separated strands and aligned segments close to one another but unbonded. The correct form, a power dependence of k2 on ionic strength, is predicted. Comparison of the theoretical exponent with data allows the conclusion that each of the two single‐stranded segments in the aligned but unbonded configuration consists of about 13–16 nucletides (not to be confused with the much smaller number of bonded base pairs in the nucleus), and that this number, denoted by Q, is possibly correlated either with a minimum length for duplex stability or with the persistence length of a single polynucleotide strand. It is suggested that experimental determination of the dependence of Q on (G+C)‐content may distinguish between these possibilities. It is also suggested that addition of sufficient amounts of divalent metal ions such as Mg2+, Ca2+, or Co2+ may reverse the dependence of k2 on ionic strength; under these conditions, k2 is predicted to decrease with about the first power of ionic strength. At fixed ionic strength, k2 should increase with increasing concentration of divalent metal ion, and, in fact, the published observation that the formation of poly(A)·2 poly(U) from poly(A)·poly(U) and poly(U) is second order in Mg2+ concentration is here correctly predicted from a priori molecular considerations. Finally, published association rate data for oligonucleotides are discussed in the present theoretical context.