Method of designing addressable array suitable for detection of nucleic acid sequence differences using ligase detection reaction

An apparatus comprising:

• a solid support having an array of positions;
• a collection of composite or encoded oligonucleotides coupled to the solid support at the array of positions, each of said composite or encoded oligonucleotides characterized by having a target-specific portion and an address, wherein the address comprises two multimer unit sequences coupled to the solid support, wherein each multimer unit sequence (1) is comprised of three consecutive subunits linked together, each subunit independently selected from the group consisting of a trimer, tetramer, pentamer, or hexamer sequence, (2) differs from other multimer unit sequences by at least two nucleotide bases in at least one of the subunits when aligned, and (3) has a Tm value greater than 24° C., wherein the collection of oligonucleotides has at least 64 different types of oligonucleotides, and wherein the collection of composite or encoded oligonucleotides does not contain:
• (1) composite or encoded oligonucleotides having an address with a melting temperature in ° C. less than 11 times the number of subunits, (2) composite or encoded oligonucleotides having an address comprised of two identical multimer unit sequences linked together and (3) two types of composite or encoded oligonucleotides with an address having the same four subunit sequences linked together in the same order without interruption;
• and one or more detectable labels coupled to at least one of the composite or encoded oligonucleotides, thereby facilitating detection of the composite or encoded oligonucleotide and its address.

A device comprising:

• a solid support having an array of positions each suitable for attachment of one or more of a collection of oligonucleotides;
• an array of oligonucleotides on the solid support at the array of positions, wherein the one or more of a collection of oligonucleotides on the solid support comprises two multimer unit sequences coupled to the solid support, wherein each multimer unit sequence is comprised of three consecutive subunits linked together, each subunit independently selected from the group consisting of a trimer, tetramer, pentamer, or hexamer sequence, wherein each multimer unit sequence has a Tm value of greater than 24° C., wherein each of the two multimer unit sequences differs from all other multimer unit sequences by at least two nucleotide bases in at least one subunit when aligned, wherein the collection of oligonucleotides has at least 64 different types of oligonucleotides, and wherein the collection of oligonucleotides does not contain:
• (1) oligonucleotides having a sequence with a melting temperature in ° C. less than 11 times the number of subunits, (2) oligonucleotides having a sequence comprised of two identical multimer unit sequences linked together and (3) two types of oligonucleotides with a sequence having the same four subunit sequences linked together in the same order without interruption, wherein one or more of the oligonucleotides of the collection is hybridized to a nucleic acid molecule comprising a complementary nucleotide sequence;
• and wherein one or more target nucleic acid molecules is coupled to one or more of the oligonucleotides of the collection.

An instrument comprising:

• a solid support comprising at least 64 types of oligonucleotides coupled to the solid support at an array of positions, wherein the one or more oligonucleotides coupled to the solid support at a position on the array comprises an address that comprises two multimer unit sequences coupled to the solid support, wherein each multimer unit sequence (1) is comprised of three consecutive subunits linked together, each subunit independently selected from the group consisting of a trimer, tetramer, pentamer, or hexamer sequence, (2) differs from the other multimer unit sequences by at least two nucleotide bases in at least one of the subunits when aligned, and (3) has a Tm value greater than 24° C., and wherein the oligonucleotides on the array do not contain:
• (1) oligonucleotides having an address with a melting temperature in ° C. less than 11 times the number of subunits, (2) oligonucleotides having an address comprised of two identical multimer unit sequences linked together and (3) two types of oligonucleotides with an address having the same four subunit sequences linked together in the same order without interruption;
• one or more nucleic acid molecules hybridized to complementary portions of the one or more oligonucleotides on said solid support;
• and an imager configured to detect the hybridized nucleic acid molecules.