Abstract:
: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.
journal_name
Biopolymersjournal_title
Biopolymersauthors
Guerra JCdoi
10.1002/bip.22214subject
Has Abstractpub_date
2013-08-01 00:00:00pages
538-47issue
8eissn
0006-3525issn
1097-0282journal_volume
99pub_type
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