Received on May 13, 2004
Accepted on August 24, 2004

Molecular Diagnostics and Genetics

Hybridization Isotherms of DNA Microarrays and the Quantification of Mutation Studies

¹ UMR 5819 [UJF, Centre National de la Recherche Scientifique (CNRS), CEA], DRFMC/SI3M, CEA Grenoble, Grenoble, France
² Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy, Russia

^* To whom correspondence should be addressed. E-mail: ahalperin{at}cea.fr.

Method: The theory is formulated in terms of the hybridization isotherms relating the hybridization fraction at the spot to the composition of the sample solutions at thermodynamic equilibrium. It focuses on samples containing an excess of single-stranded DNA and on DNA arrays with a low surface density of probes. The hybridization equilibrium constants can be obtained by the nearest-neighbor method.

Results: Two approaches allowed us to obtain quantitative results from the DNA array data. In one, the signal of the mutation spot was compared with that of the wild-type spot. The implementation requires knowledge of the saturation intensity of the two spots. The second approach required comparison of the intensity of the mutation spot at two different temperatures. In this case, knowledge of the saturation signal was not always necessary.

Conclusions: DNA arrays can be used to obtain quantitative results on the concentration ratio of mutated DNA to wild-type DNA in studies of somatic point mutations.