METHOD OF DESIGNING ADDRESSABLE ARRAY FOR DETECTION OF NUCLEIC ACID SEQUENCE DIFFERENCES USING LIGASE DETECTION REACTION

摘要

The present invention is directed to a method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, where the plural capture oligonucleotide probes have melting temperatures within a narrow range. The first step of the method involves providing a first set of a plurality of tetramers of four nucleotides linked together, where (1) each tetramer within the set differs from all other tetramers in the set by at least two nucleotide bases, (2) no two tetramers within a set are complementary to one another, (3) no tetramers within a set are palindromic or dinucleotide repeats, and (4) no tetramer within a set has one or less or three or more G or C nucleotides. Groups of 2 to 4 of the tetramers from the first set are linked together to form a collection of multimer units. From t he collection of multimer units, all multimer units formed from the same tetram er and all multimer units having a melting temperature in ~C of less than 4 tim es the number of tetramers forming a multimer unit are removed to form a modifi ed collection of multimer units. The modified collection of multimer units is arranged in a list in order of melting temperature. The order of the modifie d collection of multimer units is randomized in 2~C increments of melting temperature.