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Background: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild type DNA. This excess can give rise to false positives due to competitive hybridization of the wild type target at the mutation spot. The analysis of the DNA array data is typically qualitative aiming to establish the presence or absence of a particular point mutation. Our theoretical approach yields methods for quantifying the analysis so as to obtain the ratio of concentrations of mutated and wild type DNA. 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 low surface density of probes. The hybridization equilibrium constants can be obtained by the nearest neighbor method. Results: Two approaches allow us to obtain quantitative results from the DNA array data. In one the signal of the mutation spot is compared with that of the wild type spot. The implementation requires knowledge of the saturation intensity of the two spots. The second approach requires comparison of the intensity of the mutation spot at two different temperatures. In this case knowledge of the saturation signal is 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., Comment: To be published in Clinical Chemistry Nov. 2004. 15 pages and 8 figures

The Self-Consistent Field theory of brushes of neutral water-soluble polymers described by two-state models is formulated in terms of the effective Flory interaction parameter $\chi_{eff}(T,\phi)$ that depends on both temperature, T and the monomer volume fraction, $\phi$. The concentration profiles, distribution of free ends and compression force profiles are obtained in the presence and in the absence of a vertical phase separation. A vertical phase separation within the layer leads to a distinctive compression force profile and a minimum in the plot of the moments of the concentration profile vs. the grafting density. The analysis is applied explicitly to the Karalstrom model. The relevance to brushes of Poly(N-isopropylacrylamide)(PNIPAM) is discussed., Comment: Accepted for publication in the Journal of Chemical Physics