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Thermal equivalence of DNA duplexes for probe design

Thermal equivalence of DNA duplexes for probe design
Thermal equivalence of DNA duplexes for probe design
We present the theory of thermal equivalence in the framework of the Peyrard–Bishop model and some of its anharmonic variants. The thermal equivalence gives rise to a melting index ? which maps closely the experimental DNA melting temperatures for short DNA sequences. We show that the efficient calculation of the melting index can be used to analyse the parameters of the Peyrard–Bishop model and propose an improved set of Morse potential parameters. With this new set we are able to calculate some of the experimental melting temperatures to ± 1.2 °C. We review some of the concepts of sequencing probe design and show how to use the melting index to explore the possibilities of gene coverage by tuning the model parameters.
0953-8984
34106
Weber, Gerald
7cfc4eb7-a658-44fd-97e3-b3be79a6615f
Haslam, Niall
d4023afb-8897-4649-a6ea-996c3a9402cb
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Neylon, Cameron
697f067b-db25-4c41-9618-28f4b74f73aa
Weber, Gerald
7cfc4eb7-a658-44fd-97e3-b3be79a6615f
Haslam, Niall
d4023afb-8897-4649-a6ea-996c3a9402cb
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Neylon, Cameron
697f067b-db25-4c41-9618-28f4b74f73aa

Weber, Gerald, Haslam, Niall, Essex, Jonathan W. and Neylon, Cameron (2009) Thermal equivalence of DNA duplexes for probe design. Journal of Physics: Condensed Matter, 21 (3), 34106. (doi:10.1088/0953-8984/21/3/034106).

Record type: Article

Abstract

We present the theory of thermal equivalence in the framework of the Peyrard–Bishop model and some of its anharmonic variants. The thermal equivalence gives rise to a melting index ? which maps closely the experimental DNA melting temperatures for short DNA sequences. We show that the efficient calculation of the melting index can be used to analyse the parameters of the Peyrard–Bishop model and propose an improved set of Morse potential parameters. With this new set we are able to calculate some of the experimental melting temperatures to ± 1.2 °C. We review some of the concepts of sequencing probe design and show how to use the melting index to explore the possibilities of gene coverage by tuning the model parameters.

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Published date: 2009

Identifiers

Local EPrints ID: 149191
URI: http://eprints.soton.ac.uk/id/eprint/149191
ISSN: 0953-8984
PURE UUID: b9c56f67-8317-4998-bdae-31ded153e0e3
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

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Date deposited: 30 Apr 2010 08:57
Last modified: 17 Dec 2019 02:00

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