Oligonucleotides useful for detecting and analyzing nucleic acids of interest

Abstract

The invention features improved nucleic acids and methods for expression profiling of mRNAs, identifying and profiling of particular mRNA splice variants, and detecting mutations, deletions, or duplications of particular exons or other splice variants, e.g., alterations associated with a disease such as cancer, in a nucleic acid sample, e.g., a biological sample or a patient sample.

1 . A method for detecting the presence of one or more target nucleic acids in a sample, said method comprising incubating a labeled nucleic acid sample with one or more first nucleic acids that are 
 (i) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (ii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (iii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (iv) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (v) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (vi) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (vii) an LNA capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (viii) an LNA capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon; or    (ix) an LNA capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    or one or more populations of first nucleic acids that are    (x) a population of nucleic acid of (i)-(ix);    (xi) a population of nucleic acids that includes a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of a target nucleic acid;    (xii) a population of nucleic acids that includes a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of    a target nucleic acid; or    (xiii) a population of nucleic acids that includes a nucleic acid that is an LNA capable of hybridizing to only one exon or to only one intron of a target nucleic acid;    under conditions that allow at least one target nucleic acid to hybridize to at least one of said first nucleic acids.    
     
     
         2 . The method of  claim 1 , wherein hybridization is detected between at least 5 target nucleic acids and said first nucleic acids.  
     
     
         3 . The method of  claim 1 , further comprising identifying one or more hybridized target nucleic acids.  
     
     
         4 . The method of  claim 1 , further comprising determining the amount of one or more hybridized target nucleic acids.  
     
     
         5 . The method of  claim 4 , wherein one or more target nucleic acids are labeled with a fluorescent group, and wherein the determination of the amount of said hybridized target nucleic acid comprises one or more of the following: (a) adjusting for the varying intensity of an excitation light source used for detection of said hybridization, (b) adjusting for photobleaching of said fluorescent group, andor (c) comparing the fluorescent intensity of said hybridized target nucleic acid(s) to the fluorescent intensity of a different sample of hybridized nucleic acids.  
     
     
         6 . The method of  claim 1 , wherein said target nucleic acids are cDNA molecules reverse transcribed from a sample.  
     
     
         7 . The method of  claim 6 , wherein said target nucleic acids are fragmented using  E. Coli  Uracil-DNA Glycosylase.  
     
     
         8 . The method of  claim 7 , wherein said target nucleic acids are fragmented to an average size of 300 nucleotides.  
     
     
         9 . The method of  claim 7 , wherein said target nucleic acids are fragmented to an average size of 200 nucleotides.  
     
     
         10 . The method of  claim 7 , wherein said target nucleic acids are fragmented to an average size of 100 nucleotides.  
     
     
         11 . The method of  claim 7 , wherein said target nucleic acids are fragmented to an average size of 50 nucleotides.  
     
     
         12 . The method of  claim 1 , wherein said target nucleic acids are cRNA molecules amplified from a sample  
     
     
         13 . The method of  claim 12 , wherein said target nucleic acids are fragmented using alkaline hydrolysis.  
     
     
         14 . The method of  claim 1 , further comprising determining the presence or absence of an MRNA splice variant of interest in said sample or determining the presence or absence of a mutation, deletion, andor duplication of an exon of interest.  
     
     
         15 . The method of  claim 1 , wherein the sample comprises nucleic acids that are amplified using one or more primers specific for an exon of a target nucleic acid, and wherein said method comprises determining the presence or absence of an MRNA splice variant with said exon in said sample.  
     
     
         16 . The method of  claim 15 , wherein one or more of said primers are specific for an exon or exon-exon junction of interest, and said method comprises determining the presence or absence of a nucleic acid with said exon in said sample.  
     
     
         17 . The method of  claim 1 , wherein said first nucleic acids are covalently bonded to a solid support by reaction of a nucleoside phosphoramidite with an activated solid support, and subsequent reaction of a nucleoside phosphoramide with an activated nucleotide or nucleic acid bound to said solid support.  
     
     
         18 . The method of  claim 1 , further comprising contacting said target nucleic acid with a second nucleic acid or a population of second nucleic acids that binds to a different region of the target molecule than said first nucleic acid.  
     
     
         19 . The method of  claim 1 , further comprising performing expression profiling or comparative genomic hybridization.  
     
     
         20 . The method of  claim 1 , wherein said nucleic acid (i) is incubated with said labeled nucleic acid sample.  
     
     
         21 . The method of  claim 1 , wherein said nucleic acid (ii) is incubated with said labeled nucleic acid sample.  
     
     
         22 . The method of  claim 1 , wherein said nucleic acid (iii) is incubated with said labeled nucleic acid sample.  
     
     
         23 . The method of  claim 1 , wherein said nucleic acid (iv) is incubated with said labeled nucleic acid sample.  
     
     
         24 . The method of  claim 1 , wherein said nucleic acid (v) is incubated with said labeled nucleic acid sample.  
     
     
         25 . The method of  claim 1 , wherein said nucleic acid (vi) is incubated with said labeled nucleic acid sample.  
     
     
         26 . The method of  claim 1 , wherein said nucleic acid (vii) is incubated with said labeled nucleic acid sample.  
     
     
         27 . The method of  claim 1 , wherein said nucleic acid (viii) is incubated with said labeled nucleic acid sample.  
     
     
         28 . The method of  claim 1 , wherein said nucleic acid (ix) is incubated with said labeled nucleic acid sample.  
     
     
         29 . The method of  claim 1 , wherein in said first nucleic acid of (i)-(ix) the length of said first region and the length of said second region are between 3 and 50 nucleotides, inclusive, and said first nucleic acid of (i)-(ix) is incubated with said labeled nucleic acid sample.  
     
     
         30 . The method of  claim 29 , wherein the length of said first region and the length of said second region are between 10 and 40 nucleotides, inclusive.  
     
     
         31 . The method of  claim 30 , wherein the length of said first region and the length of said second region are between 20 and 30 nucleotides, inclusive.  
     
     
         32 . The method of  claim 1 , wherein in said first nucleic acid of (i)-(ix) said first region and said second region are of the same length, and said first nucleic acid of (i)-(ix) is incubated with said labeled nucleic acid sample.  
     
     
         33 . The method of  claim 1 , wherein in said first nucleic acid of (i)-(ix) said first region and said second region are of a different length, and said first nucleic acid of (i)-(ix) is incubated with said labeled nucleic acid sample.  
     
     
         34 . The method of  claim 1 , wherein said population of (x) is incubated with said labeled nucleic acid sample.  
     
     
         35 . The method of  claim 1 , wherein said population of (xi) is incubated with said labeled nucleic acid sample.  
     
     
         36 . The method of  claim 1 , wherein said population of (xii) is incubated with said labeled nucleic acid sample.  
     
     
         37 . The method of  claim 1 , wherein said population of (xiii) is incubated with said labeled nucleic acid sample.  
     
     
         38 . The method of  claim 1 , wherein said nucleic acid of (ii), (v) or (viii) is a non-naturally occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of a target nucleic acid, and said nucleic acid of (ii), (v) or (viii) is incubated with said labeled nucleic acid sample.  
     
     
         39 . The method of  claim 1 , wherein said nucleic acid of (ii), (v) or (viii) is a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of a target nucleic acid, and said nucleic acid of (ii), (v) or (viii) is incubated with said labeled nucleic acid sample.  
     
     
         40 . The method of  claim 1 , wherein said nucleic acid of (ii), (v) or (viii) comprises an LNA capable of hybridizing to only one exon or to only one intron of a target nucleic acid, and said nucleic acid of (ii), (v) or (viii) is incubated with said labeled nucleic acid sample.  
     
     
         41 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid is between 15 and 150 nucleotides in length, inclusive, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         42 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid is between 5 and 100 nucleotides in length, inclusive, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         43 . The method of  claim 42 , wherein said nucleic acid is between 20 and 80 nucleotides in length, inclusive.  
     
     
         44 . The method of  claim 43 , wherein said nucleic acid is between 30 and 60 nucleotides in length, inclusive.  
     
     
         45 . The method of  claim 44 , wherein said nucleic acid is 40 nucleotides in length.  
     
     
         46 . The method of  claim 44 , wherein said nucleic acid is 50 nucleotides in length.  
     
     
         47 . The method of  claim 1  wherein said nucleic acid of (i)-(ix) is between 8 and 70 nucleotides in length and is incubated with said labeled nucleic acid sample.  
     
     
         48 . The method of  claim 47  wherein said nucleic acid of(i)-(ix) is between 9 and 50 nucleotides in length.  
     
     
         49 . The method of  claim 48  wherein said nucleic acid of(i)-(ix) is between 12 and 40 nucleotides in length.  
     
     
         50 . The method of  claim 49  wherein said nucleic acid of (i)-(ix) is between 15 and 35 nucleotides in length.  
     
     
         51 . The method of  claim 1 , wherein in said population of (x)-(xiii) at least 5% of the nucleotides in said nucleic acid are LNA units, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         52 . The method of  claim 51 , wherein at least 10% of the nucleotides in said nucleic acid are LNA units.  
     
     
         53 . The method of  claim 52 , wherein at least 20% of the nucleotides in said nucleic acid are LNA units.  
     
     
         54 . The method of  claim 1 , wherein in said population of (x)-(xiii) every second nucleotide in said nucleic acid is an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         55 . The method of  claim 1 , wherein in said population of (x)-(xiii) every third nucleotide in said nucleic acid is an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         56 . The method of  claim 1 , wherein in said population of (x)-(xiii) every fourth nucleotide in said nucleic acid is an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         57 . The method of  claim 1 , wherein in said population of (x)-(xiii) every fifth nucleotide in said nucleic acid is an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         58 . The method of  claim 1 , wherein in said population of (x)-(xiii) every sixth nucleotide in said nucleic acid is an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         59 . The method of  claim 1 , wherein in said population of (x)-(xiii) every second and every third nucleotide, every second and every fourth nucleotide, every second and every fifth nucleotide, every second and every sixth nucleotide, every third and every fourth nucleotide, every third and every fifth nucleotide, every third and every sixth nucleotide, every fourth and every fifth nucleotide, every fourth and every sixth nucleotide, andor every fifth and every sixth nucleotide in said nucleic acid is an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         60 . The method of  claim 59 , wherein every second, every third, and every fourth nucleotide in said nucleic acid is an LNA unit.  
     
     
         61 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid comprises two or more contiguous LNA units, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         62 . The method of  claim 61 , wherein said nucleic acid comprises at least 4 contiguous LNA units.  
     
     
         63 . The method of  claim 62 , wherein said nucleic acid comprises at least 5 contiguous LNA units.  
     
     
         64 . The method of  claim 61 , wherein the number of contiguous LNA units is between 5 and 20% of the total length of said nucleic acid.  
     
     
         65 . The method of  claim 64 , wherein the number of contiguous LNA units is between 10 and 15% of the total length of said nucleic acid.  
     
     
         66 . The method of  claim 61 , wherein at least one LNA unit in said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid, and at least one LNA unit in said nucleic acid is capable of hybridizing to a second region within a second exon of said target nucleic acid that is adjacent to said first exon.  
     
     
         67 . The method of  claim 66 , wherein at least two LNA units in said nucleic acid hybridize to a first region within a first exon of a target nucleic acid, and at least two LNA units in said nucleic acid hybridize to a second region within a second exon of said target nucleic acid that is adjacent to said first exon.  
     
     
         68 . The method of  claim 67 , wherein at least three LNA units in said nucleic acid hybridize to a first region within a first exon of a target nucleic acid, and at least three LNA units in said nucleic acid hybridize to a second region within a second exon of said target nucleic acid that is adjacent to said first exon.  
     
     
         69 . The method of  claim 1 , wherein in said population of (x)-(xiii) the 5′ terminal nucleotide of said nucleic acid is not an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         70 . The method of  claim 1 , wherein in said population of (x)-(xiii) the 5′ terminal nucleotide of said nucleic acid is an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         71 . The method of  claim 1 , wherein in said population of (x)-(xiii) the 3′ terminal nucleotide of said nucleic acid is not an LNA unit, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         72 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid can distinguish between different nucleic acids that cannot be distinguished using a naturally-occurring control nucleic acid, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         73 . The method of  claim 72 , wherein said control nucleic acid consists of only 2′-deoxynucleotides.  
     
     
         74 . The method of  claim 72 , wherein said different nucleic acids are mRNA splice variants.  
     
     
         75 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid comprises one or more universal bases, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         76 . The method of  claim 75 , wherein said universal base is located at the 5′ or 3′ terminus of said nucleic acid.  
     
     
         77 . The method of  claim 75 , wherein one or more universal bases are located at the 5′ and 3′ termini of said nucleic acid.  
     
     
         78 . The method of  claim 75 , wherein all of said nucleic acids of said population have the same number of universal bases.  
     
     
         79 . The method of  claim 75 , wherein said universal base is inosine, pyrene, 3-nitropyrrole, or 5-nitroindole.  
     
     
         80 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid comprises at least one LNA A or LNA T, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         81 . The method of  claim 1 , wherein in said population of (x)-(xiii) each nucleic acid in said population comprises at least one LNA A or LNA T, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         82 . The method of  claim 81 , wherein all of the adenine and thymine-containing nucleotides in said LNA are LNA A and LNA T, respectively.  
     
     
         83 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid comprises a at least one 2,6,-diaminopurine or 2-thio-thymine base, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         84 . The method of  claim 1 , wherein in said population of(x)-(xiii) at least 5% of the nucleic acids in said population are LNA, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         85 . The method of  claim 1 , wherein in said population of(x)-(xiii) at least 10% of the nucleic acid in said population are LNA, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         86 . The method of  claim 1 , wherein said population of (x)-(xiii) comprises nucleic acids that together hybridize to at least 10% of the nucleic acids expressed by a particular cell or tissue, and said population of(x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         87 . The method of  claim 86 , nucleic acids together hybridize to at least 50% of the exons of a target nucleic acid.  
     
     
         88 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid does not form a hairpin that would otherwise inhibit its binding to a target nucleic acid, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         89 . The method of  claim 1 , wherein in said population of (x)-(xiii) opposing nucleotides in a palindrome pair or opposing nucleotides in inverted repeats of said nucleic acid are not both LNA units, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         90 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid forms less than 3 intramolecular base-pairs, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         91 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid does not have LNA-5-nitroindole: LNA-5-nitroindole intramolecular base-pairs, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         92 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid has a LNA unit with a 2,6,-diaminopurine, 2-aminopurine, 2-thio-thymine, 2-thio-uracil, inosine, or hypoxanthine base, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         93 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid has a 2′O, 4C-methylene linkage, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         94 . The method of  claim 1 , wherein in said population of (x)-(xiii) one or more nucleic acids are LNA/DNA, LNA/RNA, or LNA/DNA/RNA chimeras, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         95 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid has a melting temperature that is at least 10° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         96 . The method of  claim 95 , wherein said nucleic acid has a melting temperature that is at least 20° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides.  
     
     
         97 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acid has a capture efficiency that is at least 100% greater than that of the corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         98 . The method of  claim 97 , wherein said nucleic acid has a capture efficiency that is at least 400% greater than that of the corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid.  
     
     
         99 . The method of  claim 1 , wherein in said population of (x)-(xiii) said nucleic acids are covalently bonded to a solid support, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         100 . The method of  claim 99 , wherein said nucleic acids are in a predefined arrangement.  
     
     
         101 . The method of  claim 1 , wherein said population of (x)-(xiii) comprises at least 10 different nucleic acids, and said population of (x)-(xiii) is incubated with said labeled nucleic acid sample.  
     
     
         102 . The method of  claim 101 , wherein said population of (x)-(xiii) comprises at least 100 different nucleic acids.  
     
     
         103 . The method of  claim 102 , wherein said population of (x)-(xiii) comprises at least 500 different nucleic acids.  
     
     
         104 . The method of  claim 103 , wherein said population of (x)-(xiii) comprises at least 1,000 different nucleic acids.  
     
     
         105 . The method of  claim 104 , wherein said population of (x)-(xiii) comprises at least 5,000 different nucleic acids.  
     
     
         106 . A method for classifying a test nucleic acid sample comprising a target nucleic acid, said method comprising the steps of: (a) incubating a test nucleic acid sample with one or more nucleic acids probes that are (i) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon; 
 (ii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (iii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (iv) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (v) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (vi) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (vii) an LNA capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (viii) an LNA capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon; or (ix) an LNA capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    or one or more populations of first nucleic.acid probes that are (x) a population of nucleic acid of (i)-(ix);    (xi) a population of nucleic acids that includes a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of a target nucleic acid;    (xii) a population of nucleic acids that includes a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of a target nucleic acid; or (xiii) a population of nucleic acids that includes a nucleic acid that is an LNA capable of hybridizing to only one exon or to only one intron of a target nucleic acid; under conditions that allow at least one of the nucleic acids in said test sample to hybridize to at least one nucleic acid probe;    (b) detecting a hybridization pattern of said test nucleic acid sample; and    (c) comparing said hybridization pattern to a hybridization pattern of a first nucleic acid standard, whereby said comparison indicates whether or not said test sample has the same classification as said first standard.    
     
     
         107 . The method of  claim 106 , further comprising comparing a hybridization pattern of said test nucleic acid sample to a hybridization pattern of a second standard.  
     
     
         108 . The method of  claim 106 , wherein at least.5 target nucleic acids hybridize to said nucleic acid probes.  
     
     
         109 . The method of  claim 106 , further comprising identifying a hybridized target nucleic acid.  
     
     
         110 . The method of  claim 106 , further comprising determining the amount of said hybridized target nucleic acid.  
     
     
         111 . The method of  claim 106 , wherein said target nucleic acids are labeled with fluorescent groups.  
     
     
         112 . The method of  claim 111 , wherein said determination comprises scaling for the varying labeling efficiency for the different fluorescent groups used for detection of said hybridization.  
     
     
         113 . The method of  claim 111 , wherein said determination comprises adjusting for the varying intensity of the excitation light source used for detection of said hybridization.  
     
     
         114 . The method of  claim 111 , wherein said determination comprises adjusting for photobleaching of said fluorescent group.  
     
     
         115 . The method of  claim 111 , wherein said comparison comprises adjusting for a difference in the amount of said nucleic acid probes used for hybridization to said test sample and said first standard.  
     
     
         116 . The method of  claim 111 , wherein said comparison comprises adjusting for a difference in the buffer used for hybridization to said test sample and said first standard.  
     
     
         117 . The method of  claim 116 , wherein said difference is a difference in Na +  concentration.  
     
     
         118 . The method of  claim 111 , wherein said first nucleic acid standard is labeled with a different fluorescent group.  
     
     
         119 . The method of  claim 106 , wherein said target nucleic acids are cDNA molecules reverse transcribed from a sample.  
     
     
         120 . The method of  claim 119 , wherein said target nucleic acids are fragmented using  E. coli  Uracil-DNA Glycosylase.  
     
     
         121 . The method of  claim 120 , wherein said target nucleic acids are fragmented to an average size of 300 nucleotides.  
     
     
         122 . The method of  claim 120 , wherein said target nucleic acids are fragmented to an average size of 200 nucleotides.  
     
     
         123 . The method of  claim 120 , wherein said target nucleic acids are fragmented to an average size of 100 nucleotides.  
     
     
         124 . The method of  claim 120 , wherein said target nucleic acids are fragmented to an average size of 50 nucleotides.  
     
     
         125 . The method of  claim 106 , wherein said target nucleic acids are cRNA molecules amplified from a sample.  
     
     
         126 . The method of  claim 125 , wherein said target nucleic acids are fragmented using alkaline hydrolysis.  
     
     
         127 . The method of  claim 106 , further comprising determining the presence or absence of an mRNA splice variant of interest in said sample.  
     
     
         128 . The method of  claim 127 , wherein said mRNA splice variant is indicative of a disease, disorder, or condition.  
     
     
         129 . The method of  claim 128 , wherein said disease is cancer.  
     
     
         130 . The method of  claim 106 , further comprising determining the presence or absence of a mutation, deletion, andor duplication of an exon of interest.  
     
     
         131 . The method of  claim 130 , wherein said mutation, deletion, andor duplication is indicative of a disease, disorder, or condition.  
     
     
         132 . The method of  claim 131 , wherein said disease is cancer.  
     
     
         133 . The method of  claim 106 , wherein the sample comprises nucleic acids that are amplified using one or more primers specific for an exon of a target nucleic acid, and wherein said method involves determining the presence or absence of an mRNA splice variant with said exon in said sample.  
     
     
         134 . The method of  claim 133 , wherein one or more of said primers are specific for an exon or exon-exon junction of interest, and said method involves determining the presence or absence of a nucleic acid with said exon in said sample.  
     
     
         135 . The method of  claim 106 , wherein said first nucleic acids are covalently bonded to a solid support by reaction of a nucleoside phosphoramidite with an activated solid support, and subsequent reaction of a nucleoside phosphoramide with an activated nucleotide or nucleic acid bound to said solid support.  
     
     
         136 . A method of selecting a nucleic acid for a population of nucleic acids, said method comprising the steps of: 
 (a) determining the melting temperature of a nucleic acid, determining the ability of said nucleic acid to self-anneal, determining the ability of said nucleic acid to hybridize to one or more exons or introns of a target nucleic acid, andor determining the ability of said nucleic acid to hybridize to a non-target nucleic acid, and    (b) selecting said nucleic acid for inclusion or exclusion from said population based on the determination in step (a), wherein said nucleic acid is a nucleic acid that is    (i) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (ii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (iii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (iv) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (v) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (vi) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (vii) an LNA capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (viii) an LNA capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (ix) an LNA capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    or (x) a nucleic acid that has least one LNA unit and that is capable of hybridizing to only one exon or to only one intron of a target nucleic acid.    
     
     
         137 . A method of detecting a target nucleic acid in a sample, said method comprising incubating a nucleic acid sample with a fluorescently labeled nucleic acid probe that comprises: 
 (i) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (ii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (iii) a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (iv) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (v) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon;    (vi) a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    (vii) an LNA capable of hybridizing to a first region within a first exon of a target nucleic acid and to a second region within a second exon of said target nucleic acid that is adjacent to said first exon;    (viii) an LNA capable of hybridizing to a first region within an exon of a target nucleic acid and to a second region within an intron of said target nucleic acid that is adjacent to said exon; or (ix) an LNA capable of hybridizing to a first region within a first intron of a target nucleic acid and to a second region within a second intron of said target nucleic acid that is adjacent to said first intron;    or a population of fluorescently labeled nucleic acid probes that comprises:    (x) a population of nucleic acids of (i)-(ix);    (xi) a population of nucleic acids that includes a non-naturally-occurring nucleic acid with a melting temperature that is at least 3° C. higher than that of the corresponding control nucleic acid with 2′-deoxynucleotides; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of a target nucleic acid;    (xii) a population of nucleic acids that includes a non-naturally-occurring nucleic acid with a capture efficiency that is at least 10% greater than that of a corresponding control nucleic acid with 2′-deoxynucleotides at the temperature equal to the melting temperature of said nucleic acid; wherein said nucleic acid is capable of hybridizing to only one exon or to only one intron of a target nucleic acid; or    (xiii) a population of nucleic acids that includes a nucleic acid that is an LNA capable of hybridizing to only one exon or to only one intron of a target nucleic acid;    under conditions that allow at least one target nucleic acid to hybridize to at least one of said nucleic acid probes; and detecting said probes via fluorescent in situ hybridization.    
     
     
         138 . The method of  claim 137 , wherein said probe or said population of probes comprise LNA in every other or every third position of the nucleotide sequence.  
     
     
         139 . The method of  claim 137 , wherein said probe or said population of probes are used for the detection of a repetitive element.  
     
     
         140 . The method of  claim 139 , wherein said repetitive element is a centromeric alpha-repeat or a telomeric repeat.  
     
     
         141 . The method of  claim 139 , wherein said repetitive element is in human chromosome 13 or 21.  
     
     
         142 . The method of  claim 137 , wherein said probe or said population of probes are used for the detection of a single base pair difference between repetitive sequences or for the detection of single copy sequences.  
     
     
         143 . The method of  claim 142 , wherein said repetitive sequences is in human chromosome 13 or 21.  
     
     
         144 . The method of  claim 142 , wherein said repetitive element is a centromeric alpha-repeat.  
     
     
         145 . The method of  claim 137 , wherein said hybridization occurs without a denaturation step.