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Campa A, Giansanti A. Melting of DNA oligomers: dynamical models and comparison with experimental results. J Biol Phys. 1999;24(2):141-55doi: 10.1023/A:1005166612156.
Campa, A., & Giansanti, A. (1999). Melting of DNA oligomers: dynamical models and comparison with experimental results. Journal of biological physics, 24(2), 141-55. https://doi.org/10.1023/A:1005166612156
Campa, A, and Giansanti, A. "Melting of DNA oligomers: dynamical models and comparison with experimental results." Journal of biological physics vol. 24,2 (1999): 141-55. doi: https://doi.org/10.1023/A:1005166612156
Campa A, Giansanti A. Melting of DNA oligomers: dynamical models and comparison with experimental results. J Biol Phys. 1999 Jun;24(2):141-55. doi: 10.1023/A:1005166612156. PMID: 23345675; PMCID: PMC3456598.
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J Biol Phys. 1999 Jun;24(2):141-55. doi: 10.1023/A:1005166612156.

Melting of DNA oligomers: dynamical models and comparison with experimental results.

Journal of biological physics

A Campa, A Giansanti

Affiliations

  1. Physics Laboratory, Istituto Superiore di Sanità and INFN Sanità, Viale Regina Elena 299, 00161 Roma, Italy.

PMID: 23345675 PMCID: PMC3456598 DOI: 10.1023/A:1005166612156

Abstract

We compare experimental melting curves of short heterogeneous DNA oligomers with theoretical curves derived from statistical mechanics. Partition functions are computed with the one-dimensional Peyrard-Bishop (PB) Hamiltonian, already used in the study of the melting of long DNA chains. Working with short chains we take into account, in the computations, not only the breaking of the interstrand hydrogen bonds, but also the complete dissociation of the double helix into separate single strands. Since this dissociation equilibrium is of general relevance, independent of the particular microscopic model, we give some details of its treatment. We discuss how the non bonded three-dimensional interactions, not explicitly considered in the one-dimensional PB model, are taken into account through the treatment of the dissociation equilibrium. We also evaluate the relevance of the dissociation as a function of the chain length.

Keywords: Dissociation equilibrium; melting; non-bonded interactions; nonlinear models; oligonucleotides; short duplex DNA

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