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Terminal contributions for duplex oligonucleotide thermodynamic properties in the context of nearest neighbor models
Author(s) -
Guerra João Carlos de Oliveira,
Licínio Pedro
Publication year - 2011
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.21560
Subject(s) - oligomer , chemistry , enthalpy , dimer , thermodynamics , duplex (building) , k nearest neighbors algorithm , entropy (arrow of time) , statistical physics , dna , physics , computer science , biochemistry , organic chemistry , artificial intelligence
Additive physical properties of DNA polymer duplexes have been expanded in terms of eight irreducible parameters that ultimately lead to consistency relations among the corresponding 10 duplex dimer contributions. End parameters are often added to allow for oligomer analysis which would add four extra degrees of freedom to the aforementioned parameters. Analysis of sufficient experimental data on oligomer duplexes allows for the unambiguous recovery of irreducible parameters. Values for free energy, enthalpy, and entropy are thus obtained, in terms of either irreducible or dimer decomposition sets. Here, a better adjust for the entropic (and enthalpic) irreducible parameters are obtained as we consider the more precise melting temperature data for the sequences of a given dataset. However, still large error estimates, and no clear distinction between the orientations of the terminal base pairs could yet be found. Finally, statistical mechanics approaches are applied for to connect the nearest neighbor approach to the two states model. Ad hoc end effects can be thus correlated to nucleation phenomena, leading to a critique for its role in nearest neighbor modeling. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 194–201, 2011.