Methods and composition to generate unique sequence DNA probes, labeling of DNA probes and the use of these probes

A method for producing a repeat depleted nucleic acid probe set which is complementary to a sequence of interest comprising the steps of:

• (a) amplifying fragments of a source polynucleotide, wherein the source polynucleotide contains the sequence of interest and wherein the fragments have sequences which are (i) unique, (ii) repetitive or (iii) a combination of unique and repetitive;
• and
• (b) hybridizing the repetitive sequences with complementary DNA having excessive amounts of repetitive sequences, thereby forming double stranded DNA with repetitive sequence;
• (c) digesting the double stranded DNA, resulting in a mixture of fragments with single stranded DNA fragments depleted of repetitive sequences and digested DNA;
• and
• (d) amplifying the single stranded DNA fragments to produce a nucleic acid probe set which is complementary to at least a portion of the sequence of interest.

A method for detecting the presence of a sequence of interest in a sample comprising:

• (1) adding a nucleic acid probe set to the sample, wherein the probe set is produced by the steps of
• (a) amplifying fragments of a source polynucleotide, wherein the source polynucleotide comprises the sequence of interest and wherein the fragments have sequences which are (i) unique, (ii) repetitive or (iii) a combination of unique and repetitive;
• and
• (b) hybridizing the repetitive sequences with complementary DNA having excessive amounts of repetitive sequences, thereby forming double stranded DNA with repetitive sequence;
• (c) digesting the double stranded DNA, resulting in a mixture of fragments with single stranded DNA fragments which are depleted of repetitive sequences and digested DNA;
• and
• (d) amplifying the single stranded DNA to produce nucleic acid probes complementary to the sequence of interest;
• and
• (2) detecting hybridization of the probe set to the sample, thereby detecting the presence of the sequence of interest in the sample.