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Slow relaxational processes in the melting of linear biopolymers: A theory and its application to nucleic acids
Author(s) -
Anshelevich V. V.,
Vologodskii A. V.,
Lukashin A. V.,
FrankKamenetskii M. D.
Publication year - 1984
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.360230105
Subject(s) - chemistry , non equilibrium thermodynamics , thermodynamics , polynucleotide , melting temperature , melting curve analysis , melting point , equilibrium constant , isothermal process , physics , materials science , organic chemistry , polymerase chain reaction , biochemistry , gene , composite material
We treat the problem of the mean time of complete separation of complementary chains of a duplex containing N base pairs. A combination of analytical and computer methods is used to obtain the exact solution in the form of a compact expression. This expression is used to analyze the limits of application of the equilibrium theory of helix–coil transition in oligo‐ and polynucleotides. It also allows the melting behavior of a biopolymer to be predicted when its melting is nonequilibrium. In the case of oligonucleotides for which the equilibrium melting takes place at a high value of the stability constant s , the general expression turns into the equation of Craig, Crothers, and Doty, used by them to determine the rate constant k f of the growth of a helical region from temperature‐jump experiments. For the case of fragmented DNA with N ∼ 10 2 , the melting process is shown to be completely nonequilibrium, and as a result, the observed melting temperature should be higher than that for the equilibrium. A simple equation is obtained that makes possible calculation of the real, “kinetic” melting temperature T k . As N increases, the observed melting temperature should approach the equilibrium value, T m . This analysis has explained quantitatively the peculiar chain‐length dependence of the experimentally observed shift in the DNA melting temperature during fragmentation. A thorough analysis is given of the nonequilibrium effects in the melting process of long DNA molecules ( N ≳ 10 3 ). The main conclusion is that even in the presence of profound hysteresis phenomena, the melting profile observed on heating may differ only slightly from the equilibrium profile.