New Brunswick, New Jersey 08903
Synopsis
The bimolecular rate constant k z 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 k z 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 nucleotides (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 k z on ionic strength; under these conditions, kZ is predicted to decrease with about the first power of ionic strength. At fixed ionic strength, k z 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.