Instituto de Física, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
Biopolymers. 2011 Mar;95(3):194-201. doi: 10.1002/bip.21560.
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.
DNA 聚合物双链体的附加物理性质已扩展到八个不可约参数，这些参数最终导致相应的 10 个双链体二聚体贡献之间的一致性关系。末端参数通常会添加，以允许进行寡聚物分析，这将为上述参数增加四个额外的自由度。对寡聚物双链体的充分实验数据的分析允许明确恢复不可约参数。因此，可以根据不可约或二聚体分解集获得自由能、焓和熵的值。在这里，我们考虑了给定数据集序列的更精确的熔点数据，从而对熵（和焓）不可约参数进行了更好的调整。然而，仍然存在较大的误差估计，并且仍然无法清楚地区分末端碱基对的方向。最后，统计力学方法被应用于将最近邻方法与两种状态模型联系起来。因此，可以将特定的末端效应与成核现象相关联，从而对其在最近邻建模中的作用提出批评。
