Oligonucleotide Paints

A method of making a set of oligonucleotide paints comprising:

• providing at least one solid support having a plurality of synthetic, single stranded oligonucleotide sequences attached thereto, wherein a portion of each of the plurality of synthetic, single stranded oligonucleotide sequences is complementary to a portion of a specific chromosome sequence, and wherein each specific chromosome sequence excludes highly repetitive elements;
• synthesizing a plurality of complementary strands, each of which is complementary to a synthetic, single stranded oligonucleotide sequence attached to the at least one solid support;
• removing the plurality of complementary strands from the at least one solid support;
• amplifying the plurality of complementary strands;
• and
• labelling the plurality of complementary strands to produce a set of oligonucleotide paints.

A method of making a set of oligonucleotide paints comprising:

• providing at least one solid support having a plurality of synthetic, single-stranded oligonucleotide sequences attached thereto, wherein a portion of each of the plurality of synthetic, single-stranded oligonucleotide sequences is complementary to a portion of a specific chromosome sequence;
• removing the plurality of synthetic oligonucleotide sequences from the at least one solid support;
• amplifying the plurality of synthetic oligonucleotide sequences to generate amplified, synthetic oligonucleotide sequences;
• and
• labelling the amplified, synthetic oligonucleotide sequences to produce a set of oligonucleotide paints, wherein each oligonucleotide paint has a resolution of about two kilobases or fewer.

A method of preparing a plurality of high resolution oligonucleotide paints comprising:

• computationally determining genomic spacing of a plurality of synthetic, oligonucleotide sequences, wherein each of the plurality is complementary to a portion of a specific chromosome sequence;
• synthesizing the plurality of synthetic oligonucleotide sequences;
• and
• labelling the plurality of synthetic oligonucleotide sequences with a detectable label to produce a plurality of oligonucleotide paints, wherein the set of oligonucleotide paints has a resolution of about two kilobases or fewer, and wherein each of a plurality of the oligonucleotide paints is complementary to a target nucleic acid sequence of 40 consecutive nucleotide bases or fewer.

A method of making a set of high resolution oligonucleotide paints comprising:

• providing at least one solid support having a plurality of synthetic, single stranded oligonucleotide sequences attached thereto, wherein a portion of each of the plurality of synthetic, single stranded oligonucleotide sequences is complementary to a portion of a specific chromosome sequence;
• synthesizing a plurality of complementary strands, each of which is complementary to a synthetic, single stranded oligonucleotide sequence attached to the at least one solid support;
• removing the plurality of complementary strands from the at least one solid support;
• amplifying the plurality of complementary strands;
• and
• labelling the plurality of complementary strands to produce a set of high resolution oligonucleotide paints, wherein each of a plurality of the oligonucleotide paints is complementary to a target nucleic acid sequence of 40 consecutive nucleotide bases or fewer.