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Calculation of nucleation free energy for duplex oligomers in the context of nearest neighbor models
Author(s) -
Oliveira Guerra João Carlos
Publication year - 2013
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.22214
Subject(s) - nucleation , chemistry , dimer , oligomer , statistical physics , k nearest neighbors algorithm , duplex (building) , context (archaeology) , consistency (knowledge bases) , thermodynamics , degrees of freedom (physics and chemistry) , physics , dna , computer science , artificial intelligence , polymer chemistry , biology , paleontology , biochemistry , organic chemistry
Additive physical properties of DNA double strand polymers have been expanded in terms of 8 irreducible parameters. This provided consistency relations among the corresponding 10 duplex dimer contributions. To allow for oligomer analysis, end parameters were often added, and this would add extra degrees of freedom to the fore mentioned parameters. Statistical mechanics approaches were then connected to the nearest neighbor (NN) approach in the framework of the two‐states model. Ad hoc end effects were thus (wrongly) correlated to nucleation phenomena and this lead to a critique for its role in NN modeling. With this motivation, a new NN model is proposed that accommodates the nucleation free energies. The model relates the nucleation free energy to the mean composition of the chain and permits to obtain a good estimate for the free energy associated only to the Watson–Crick base pairings. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 538–547, 2013.