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Bioinformatics Advance Access originally published online on June 9, 2005
Bioinformatics 2005 21(16):3333-3339; doi:10.1093/bioinformatics/bti530
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Thermodynamic properties of DNA sequences: characteristic values for the human genome

Ryan T. Koehler * and Nicolas Peyret

Applied Biosystems 850 Lincoln Centre Drive, Foster City, CA 94404, USA

*To whom correspondence should be addressed.

Motivation: Central to many molecular biology techniques as ubiquitous as PCR and Southern blotting is the design of oligonucleotide (oligo) probes and/or primers possessing specific thermodynamic properties. Here, we use validated theoretical methods to generate distributions of predicted thermodynamic properties for DNA oligos of various lengths. These distributions facilitate immediate appreciation of typical thermodynamic values for oligos of various lengths.

Results: Distributions of melting temperature (Tm), free energy , and fraction hybridized or fraction bound (Fb), are presented for oligos of length 10–50 bases sampled from the human genome. The effects of changing temperature, oligo and salt concentrations, constraining G+C content, and introducing mismatches are exemplified. Our results provide the first survey of typical and limiting thermodynamic values evaluated on a genomic scale. Described numbers comprise useful ‘rules of thumb’ that are applicable to most technologies dependent upon DNA oligo design.

Contact:Koehlert{at}appliedbiosystems.com

Supplementary information: Supplementary Data is available at http://bioinformatics.oxfordjournals.org

Received on April 6, 2005; revised on May 13, 2005; accepted on June 6, 2005

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