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 first set differs from all
other tetramers in the first set by at least two nucleotide bases, (2) no
two tetramers within the first set are complementary to one another, (3)
no tetramers within the first set are palindromic or dinucleotide
repeats, and (4) no tetramer within the first 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 the collection of multimer units, all multimer units formed from the
same tetramer and all multimer units having a melting temperature in
.degree. C. of less than 4 times the number of tetramers forming a
multimer unit are removed to form a modified collection of multimer
units. The modified collection of multimer units is arranged in a list in
order of melting temperature. The order of the modified collection of
multimer units is randomized in 2.degree. C. increments of melting
temperature.