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On the application of polyelectrolyte limiting laws to the helix–coil transition of DNA. V. Ionic effects on renaturation kinetics
Author(s) -
Manning Gerald S.
Publication year - 1976
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1976.360150709
Subject(s) - ionic strength , polynucleotide , chemistry , polyelectrolyte , divalent , ionic bonding , crystallography , persistence length , limiting , ion , thermodynamics , chemical physics , molecule , aqueous solution , polymer , physics , organic chemistry , biochemistry , mechanical engineering , engineering
The bimolecular rate constant k 2 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 2 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 Mg 2+ , Ca 2+ , or Co 2+ may reverse the dependence of k 2 on ionic strength; under these conditions, k 2 is predicted to decrease with about the first power of ionic strength. At fixed ionic strength, k 2 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 Mg 2+ concentration is here correctly predicted from a priori molecular considerations. Finally, published association rate data for oligonucleotides are discussed in the present theoretical context.