Oligonucleotide Paints

Abstract

Novel methods for making high resolution oligonucleotide paints are provided. Novel, high resolution oligonucleotide paints are also provided.

What is claimed is: 
     
         1 . A method comprising:
 a) contacting an oligonucleotide paint to a target nucleic acid sequence within a cell, the oligonucleotide paint comprising:   a single stranded nucleic acid of 20 to 1000 nucleotide bases in length, comprising, in order from 5′ to 3′: a first region, a second region, and a third region;   wherein the second region is 10 to 100 nucleotide bases in length and comprises a sequence that hybridizes to the target nucleic acid sequence under stringent hybridization conditions;   wherein the first and third regions are each independently 5 to 500 nucleotide bases in length, are not complementary to the target nucleic acid sequence, and are not complementary to regions immediately flanking the target nucleic acid sequence;   wherein at least one of the first region and third region comprises an amplification site;   b) incubating the contacted target nucleic acid sequence and oligonucleotide paint under stringent conditions to effect specific hybridization of the second region of the oligonucleotide paint to the target;   c) detecting the hybridized oligonucleotide paint.   
     
     
         2 . The method of  claim 1 , wherein the second region of the oligonucleotide paint is as least 40 nucleotides in length, and is complementary to a target nucleic acid sequence of 40 consecutive bases or fewer. 
     
     
         3 . The method of  claim 1 , wherein the second region of the oligonucleotide paint is at least 30 nucleotides in length, and is complementary to a target nucleic acid sequence of 30 consecutive bases or fewer. 
     
     
         4 . The method of  claim 1 , wherein the second region of the oligonucleotide paint is at least 20 nucleotides in length, and is complementary to a target nucleic acid sequence of 20 consecutive bases or fewer. 
     
     
         5 . The method of  claim 1 , wherein the second region of the oligonucleotide paint is at least 10 nucleotides in length, and is complementary to a target nucleic acid sequence of 10 consecutive bases or fewer. 
     
     
         6 . The method of  claim 1 , wherein the second region of the oligonucleotide paint is between 30 to 40 nucleotide bases in length, and is complementary to a target nucleic acid sequence of consecutive bases of the same length or fewer. 
     
     
         7 . The method of  claim 1 , wherein the first region and the third regions comprise a single stranded nucleic acid sequence of 10 to 200 nucleotide bases in length. 
     
     
         8 . The method of  claim 1 , wherein the oligonucleotide paint comprises one or more of a detectable label, and a retrievable label. 
     
     
         9 . The method of  claim 1 , wherein detecting the hybridized oligonucleotide paint comprises hybridizing a complementary nucleic acid sequence to the at least one amplification site. 
     
     
         10 . The method of  claim 9 , wherein the complementary nucleic sequence comprises a primer. 
     
     
         11 . The method of  claim 9 , wherein the complementary nucleic acid sequence comprises a detectable label or a retrievable label (label), and detecting the hybridized oligonucleotide paint comprises detecting the label. 
     
     
         12 . The method of  claim 11 , wherein the label comprises one or more of an enzyme, prosthetic group, luminescent marker, bioluminescent marker, fluorescent marker, radiolabel, biotin a polypeptide epitope, or an antibody. 
     
     
         13 . The method of  claim 9 , wherein the complementary nucleic acid sequences comprises one or more of a chemical cross-linker, an intercalator, and a molecular cage. 
     
     
         14 . The method of  claim 1 , wherein the cell is a human cell. 
     
     
         15 . A method comprising:
 a) contacting a pool of oligonucleotide paints to target nucleic acid sequences within a cell, each oligonucleotide paint comprising:   a single stranded nucleic acid of 20 to 1000 nucleotide bases in length, comprising, in order from 5′ to 3′: a first region, a second region, and a third region;   wherein the second region is 10 to 100 nucleotide bases in length and comprises a sequence that is that hybridizes to the target nucleic acid sequence under stringent hybridization conditions;   wherein each oligonucleotide paint in the pool is hybridizes to a different target sequence;   wherein the first and third regions are each independently 5 to 500 nucleotide bases in length, are not complementary to the target nucleic acid sequence, and are not complementary to regions immediately flanking the target nucleic acid sequence;   wherein at least one of the first region and third region comprises an amplification site;   b) incubating the contacted target nucleic acids and oligonucleotide paints under stringent conditions to effect specific hybridization of the second region of the oligonucleotide paints to their respective targets;   c) detecting the hybridized oligonucleotide paints.   
     
     
         16 . The method of  claim 15 , wherein each oligonucleotide paint in the pool comprises one or more of a detectable label and a retrievable label. 
     
     
         17 . The method of  claim 15 , wherein detecting the hybridized oligonucleotide paints comprises hybridizing complementary nucleic acid sequences to at least one amplification site of the oligonucleotide paints in the pool. 
     
     
         18 . The method of  claim 17 , wherein the complementary nucleic acid sequence comprises a label. 
     
     
         19 . The method of  claim 15 , further comprising karyotyping the cell. 
     
     
         20 . The method of  claim 15 , further comprising detecting a chromosomal aberration in the cell.