Method for estimating the probe-target affinity of a DNA chip and method for manufacturing a DNA chip

摘要

A method for estimating the affinity ϕ of a first DNA strand, or “probe”, to be hybridized with a second DNA strand, or “target”, to form a hybrid of length L_bp, the method comprising: in each division of a set of M divisions of the hybrid, counting the number of times in which each hybrid of a set of P DNA strand hybrids is present in the division, the hybrids being of length k less than the length L_bp, or “k-hybrids”; for each combination of mismatches of a set of L combinations of mismatches in a hybrid of length Lbp, determining whether the pair of mismatches is present in the hybrid; and calculating the affinity ϕ according to the relation:; $$ \varphi =\sum _{m=1}^M\sum _{p=1}^P{x}_{m,p}·{\hat{\beta }}_{m,p}+\alpha .$$