Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions.
BACKGROUND
In order to assess the stability of DNA-DNA hybridizations-for example during PCR primer design or oligonucleotide selection for microarrays-one needs to predict the change in Gibbs free energy DeltaG during hybridization. The nearest neighbor model provides a good compromise between accuracy and computational simplicity for this task. To determine optimal combinations of reaction parameters (temperature, salt concentration, oligonucleotide length and GC-content), one would like to understand how DeltaG depends on all of these parameters simultaneously.


RESULTS
We derive analytic results about the distribution of nearest neighbor DeltaG values for a Bernoulli random sequence model (specified by oligonucleotide length and average GC-content) under given experimental conditions. We find that the distribution of DeltaG values is approximately Gaussian and provide exact formulas for expectation and variance.
Rahmann
Sven
S
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany. Sven.Rahmann@cebitec.uni-bielefeld.de
Gräfe
Christine
C
D001482:Base Composition; D003198:Computer Simulation; D015342:DNA Probes / Q000737:chemistry*; D004735:Energy Transfer; D008956:Models, Chemical; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013269:Stochastic Processes; D013696:Temperature; D013816:Thermodynamics
D015342:DNA Probes; D009841:Oligonucleotides