Patent ID: 7539579

Claim:
A method for designing and selecting oligonucleotide probes for use in DNA microarrays, using a computer program product-having program instructions executable on a computer, comprising the steps: (a) inputting target DNA sequences; (b) creating an internal DNA database table that includes the entire target DNA sequences from which oligonucleotide probes are selected; (c) generating a primary table of oligonucleotide probes that contains all possible probes of a defined length that can be derived from said internal DNA database table; (d) applying user-defined selection criteria to the probes contained in said primary table of oligonucleotide probes to generate a secondary table of oligonucleotide probes therefrom, said user-defined selection criteria including compositional and thermodynamic properties; (e) evaluating the sequence similarity between probes of said secondary table and said inputted target DNA sequences, to generate a table of oligonucleotide probes of optimized sequence specificity; and (f) performing virtual hybridization of said oligonucleotide probes of optimized sequence specificity against said inputted target DNA sequences, wherein a nearest-neighbor predicted thermodynamic model of duplex formation is used to identify the sites of hybridization of said oligonucleotides within the target DNA sequences, including sites of perfectly matched hybrids as well as stably mismatched hybrids sequences, comprising; (i) selecting a minimal value (minbasescom) for the number of complementary bases between probes and potential hybridization sites, wherein said minbasescom is defined as 2≦minbasescom≦L (a given probe length); (ii) selecting a minimal value (minblocksize) for the length of contiguously paired bases within potential hybridization sites, wherein said minblocksize is specified as 2≦minblocksize≦L (a given probe length); (iii) selecting potential hybridization sites by evaluating the complementarity degree between said oligonucleotide probes and potential hybridization sites along the target sequences, wherein said potential hybridization sites are defined as sites where the number of complementary bases between the probe and the evaluated sites is equal to or greater than minbasescom or sites where a block of contiguously paired bases is equal to or greater than minblocksize; (iv) calculating the free energy value (ΔG°) for the duplex stability of probes paired with their respective potential hybridization sites using said nearest-neighbor thermodynamic model of duplex formation; and (v) selecting sites of high hybridization probability, wherein said sites of high hybridization probability are potential hybridization sites corresponding to probe-target duplexes with (ΔG°) values equal to or lower than pre-determined ΔG° cutoff values; and (g) showing to the user sequences for oligonucleotide probes selected by the virtual hybridization of step (f), wherein the selected oligonucleotide probes are designed to hybridize to the target DNAs in DNA microarrays.