Methods and compositions for analyzing nucleic acids

Abstract

The present invention relates to methods and compositions for analyzing nucleic acids. In particular, the invention provides for methods and combinations for analyzing nucleic acids in a plurality of samples using a plurality of detectably different signature labels and a probe that is hybridizable to each of the target nucleic acids. The invention also provides for a method for quantifying a nucleic acid by analyzing the amount of a label, e.g., a photoactivatable label, attached to the target nucleic acid.

What is claimed is:  
     
         1 . A method for analyzing nucleic acids in a plurality of samples, which method comprises: 
 a) attaching each of target nucleic acids, if there is one in a sample, in a plurality of samples with a signature label separately whereby said target nucleic acid in each of said plurality of samples is attached to a detectably different signature label;    b) pooling said labeled target nucleic acids in different samples into a single mixture;    c) hybridizing each of said labeled target nucleic acids in said single mixture with a probe that is hybridizable to each of said labeled target nucleic acids in a single reaction to form a plurality of target nucleic acid/probe duplexes; and    d) determining presence or absence, amount and/or identity of said target nucleic acid in each of said plurality of samples by analyzing presence or absence, amount and/or identity of said signature label in each of said target nucleic acid/probe duplexes.    
     
     
         2 . The method of  claim 1 , wherein the labels are selected from the group consisting of a mass group, a metal, a fluorescent group, a luminescent group, a chemiluminescent group, an optical group, a charge group, a polar group, a color, a hapten, an antibody, an epitope-containing compound, a protein binding ligand, a nucleotide sequence, a radioactive group, an enzyme, an enzyme substrate, a particulate particle, magnetically responsive compound and a combination thereof.  
     
     
         3 . The method of  claim 1 , wherein the labels are same kind or different kinds of substances.  
     
     
         4 . The method of  claim 1 , wherein the labels are composites made of a plurality of substances and the labels are different from each other because they contain different kinds of substances having different chemical or physical composition or properties and/or contain same kinds of substances at different ratios.  
     
     
         5 . The method of  claim 1 , wherein at least one of the samples is a biological, an agricultural, an veterinary, an environmental, or a human sample.  
     
     
         6 . The method of  claim 5 , wherein the biological sample is a clinical sample.  
     
     
         7 . The method of  claim 1 , wherein at least one of the target nucleic acids is a nucleic acid amplification product.  
     
     
         8 . The method of  claim 1 , wherein the labels are attached to the target nucleic acids covalently or non-covalently.  
     
     
         9 . The method of  claim 1 , wherein the labels are attached to the target nucleic acids directly or indirectly via a linker.  
     
     
         10 . The method of  claim 1 , wherein the labels are attached to the target nucleic acids via a cleavable linkage or linker.  
     
     
         11 . The method of  claim 10 , wherein the linkage or linker is cleavable via a physical, a chemical or an enzymatic treatment.  
     
     
         12 . The method of  claim 1 , wherein the probe is immobilized on a surface and the target nucleic acids and the probe are hybridized on said surface.  
     
     
         13 . The method of  claim 12 , wherein the probe is immobilized in a plurality of areas on the surface.  
     
     
         14 . The method of  claim 1 , wherein the target nucleic acids and the probe are hybridized in a liquid.  
     
     
         15 . The method of  claim 14 , wherein the hybridization is conducted in a liquid container selected from the group consisting of a beaker, a flask, a cylinder, a test tube, an eppendorf tube, a centrifugation tube, a culture dish and a multiwell plate.  
     
     
         16 . The method of  claim 1 , wherein the pooling step is conducted prior to or concurrently with the hybridizing step.  
     
     
         17 . The method of  claim 1 , wherein the pooling step is conducted after the hybridizing step but prior to or concurrently with the determining step.  
     
     
         18 . The method of  claim 1 , wherein at least one of the signature labels is contained in a composition comprising said signature label and a binding ligand that facilitates attachment of said signature label to a target nucleic acid.  
     
     
         19 . The method of  claim 18 , wherein the binding ligand comprises a chemical moiety that binds to a target nucleic acid and that, when activated by light, forms at least one covalent bond with the target nucleic acid.  
     
     
         20 . The method of  claim 19 , wherein the binding ligand is an intercalator.  
     
     
         21 . The method of  claim 20 , wherein the intercalator is a furocoumarin, a phenanthridine, a monoadduct forming compound or an angelicin derivative.  
     
     
         22 . The method of  claim 19 , wherein the binding ligand is a non-intercalator.  
     
     
         23 . The method of  claim 22 , wherein the non-intercalator is selected from the group consisting of a benzimide, a netropsin and a distamycin.  
     
     
         24 . The method of  claim 19 , wherein the binding ligand is a photoreactive binding ligand.  
     
     
         25 . The method of  claim 18 , wherein the composition further comprises a binding enhancer that has a specific affinity for nucleic acids.  
     
     
         26 . The method of  claim 25 , wherein the binding enhancer is an intercalator or a non-intercalator.  
     
     
         27 . The method of  claim 26 , wherein the intercalator is a monoadduct forming compound.  
     
     
         28 . The method of  claim 26 , wherein the non-intercalator is selected from the group consisting of an oligo pyrrole, a phenyl indole, a nucleic acid and a protein.  
     
     
         29 . The method of  claim 25 , wherein the binding enhancer has an affinity for nucleic acids equal to or greater than 1×10 4  mole −1 , specifically binds to nucleic acids in the presence of greater than 10 mM magnesium or comprises a nucleotide sequence that specifically binds to a target nucleic acid to be analyzed.  
     
     
         30 . The method of  claim 1 , further comprising a step of releasing target nucleic acids from a sample source.  
     
     
         31 . The method of  claim 30 , wherein the target nucleic acids are released and labeled concurrently using a composition comprising a signature label and a lysing agent for releasing nucleic acids.  
     
     
         32 . The method of  claim 25 , wherein both the binding ligand and the binding enhancer are intercalator moieties and wherein at least one of said intercalator moieties forms at least one covalent bond with a nucleic acid to be analyzed.  
     
     
         33 . The method of  claim 25 , wherein the composition further comprises a lysing reagent for releasing a target nucleic acid to be analyzed.  
     
     
         34 . The method of  claim 25 , wherein the binding ligand, binding enhancer and signature label in at least one of the compositions are bound together in the form of a covalent or noncovalent complex.  
     
     
         35 . The method of  claim 34 , wherein the signature label is linked to the binding ligand and/or binding enhancer in the complex directly or indirectly via a linker.  
     
     
         36 . The method of  claim 34 , wherein the signature label is linked to the binding ligand and/or binding enhancer in the complex via a cleavable linkage or linker.  
     
     
         37 . The method of  claim 36 , wherein the linkage or linker is cleavable via a physical, a chemical or an enzymatic treatment.  
     
     
         38 . A combination for analyzing nucleic acids in a plurality of samples, which combination comprises a plurality of detectably different signature labels, wherein each of said signature labels is capable of being attached to a target nucleic acid to be analyzed.  
     
     
         39 . The combination of  claim 38 , wherein the labels are selected from the group consisting of a mass group, a metal, a fluorescent group, a luminescent group, a chemiluminescent group, an optical group, a charge group, a polar group, a color, a hapten, an antibody, an epitope-containing compound, a protein binding ligand, a nucleotide sequence, a radioactive group, an enzyme, an enzyme substrate, a particulate particle, magnetically responsive compound and a combination thereof.  
     
     
         40 . The combination of  claim 38 , wherein the labels are same kind or different kinds of substances.  
     
     
         41 . The combination of  claim 38 , wherein the labels are composites made of a plurality of substances and the labels are different from each other because they contain different kinds of substances having different chemical or physical composition or properties and/or contain same kinds of substances at different ratios.  
     
     
         42 . The combination of  claim 38 , wherein at least one of the signature labels is contained in a composition comprising said signature label and a binding ligand that facilitates attachment of said signature label to a target nucleic acid  
     
     
         43 . The combination of  claim 42 , wherein the binding ligand comprises a chemical moiety that binds to a target nucleic acid and that, when activated by light, forms at least one covalent bond with the target nucleic acid.  
     
     
         44 . The combination of  claim 42 , wherein the binding ligand is an intercalator or a non-intercalator.  
     
     
         45 . The combination of  claim 44 , wherein the intercalator is a furocoumarin, a phenanthridine, a monoadduct forming compound or an angelicin derivative.  
     
     
         46 . The combination of  claim 44 , wherein the non-intercalator is selected from the group consisting of a benzimide, a netropsin and a distamycin.  
     
     
         47 . The combination of  claim 42 , wherein the binding ligand is a photoreactive binding ligand.  
     
     
         48 . The combination of  claim 42 , wherein the composition further comprises a binding enhancer that has a specific affinity for nucleic acids.  
     
     
         49 . The combination of  claim 48 , wherein the binding enhancer is an intercalator or a non-intercalator.  
     
     
         50 . The combination of  claim 49 , wherein the intercalator is a monoadduct forming compound.  
     
     
         51 . The combination of  claim 49 , wherein the non-intercalator is selected from the group consisting of an oligo pyrrole, a phenyl indole, a nucleic acid and a protein.  
     
     
         52 . The combination of  claim 48 , wherein the binding enhancer has an affinity for nucleic acids equal to or greater than 1×10 4  mole −1 , specifically binds to nucleic acids in the presence of greater than 10 mM magnesium or comprises a nucleotide sequence that specifically binds to a target nucleic acid to be analyzed.  
     
     
         53 . The combination of  claim 48 , wherein both the binding ligand and the binding enhancer are intercalator moieties and wherein at least one of said intercalator moieties forms at least one covalent bond with a nucleic acid to be analyzed.  
     
     
         54 . The combination of  claim 48 , wherein the composition further comprises a lysing reagent for releasing a target nucleic acid to be analyzed.  
     
     
         55 . The combination of  claim 48 , wherein the binding ligand, binding enhancer and signature label in at least one of the compositions are bound together in the form of a covalent or noncovalent complex.  
     
     
         56 . The combination of  claim 55 , wherein the signature label is linked to the binding ligand and/or binding enhancer in the complex directly or indirectly via a linker.  
     
     
         57 . The combination of  claim 55 , wherein the signature label is linked to the binding ligand and/or binding enhancer in the complex via a cleavable linkage or linker.  
     
     
         58 . The combination of  claim 57 , wherein the linkage or linker is cleavable via a physical, a chemical or an enzymatic treatment.  
     
     
         59 . A method for quantifying a nucleic acid, which method comprises attaching a photoactivatable label to a target nucleic acid and determining amount of said target nucleic acid by analyzing amount of said label attached to said target nucleic acid.  
     
     
         60 . The method of  claim 59 , wherein the label is contained in a composition comprising said label and a binding ligand that facilitates attachment of said label to a target nucleic acid.  
     
     
         61 . The method of  claim 59 , wherein the label is selected from the group consisting of a mass group, a metal, a fluorescent group, a luminescent group, a chemiluminescent group, an optical group, a charge group, a polar group, a color, a hapten, an antibody, an epitope-containing compound, a protein binding ligand, a nucleotide sequence, a radioactive group, an enzyme, an enzyme substrate, a particulate particle, magnetically responsive compound and a combination thereof.  
     
     
         62 . The method of  claim 59 , wherein the label comprises same kind or different kinds of substance(s).  
     
     
         63 . The method of  claim 59 , wherein the target nucleic acid is DNA, RNA, PNA or a combination thereof.  
     
     
         64 . The method of  claim 59 , wherein the target nucleic acid is derived from a biological, an agricultural, an veterinary, an environmental, a human or a clinical sample.  
     
     
         65 . The method of  claim 59 , wherein the target nucleic acid is a nucleic acid amplification product.  
     
     
         66 . The method of  claim 59 , wherein the label is attached to the target nucleic acid covalently or non-covalently.  
     
     
         67 . The method of  claim 59 , wherein the label is attached to the target nucleic acid directly or indirectly via a linker.  
     
     
         68 . The method of  claim 67 , wherein the label is attached to the target nucleic acid via a cleavable linkage or linker.  
     
     
         69 . The method of  claim 68 , wherein the linkage or linker is cleavable via a physical, a chemical or an enzymatic treatment.  
     
     
         70 . The method of  claim 60 , wherein the binding ligand comprises a chemical moiety that binds to a target nucleic acid and that, when activated by light, forms at least one covalent bond with the target nucleic acid.  
     
     
         71 . The method of  claim 70 , wherein the binding ligand is an intercalator or a non-intercalator.  
     
     
         72 . The method of  claim 60 , wherein the binding ligand is a photoreactive binding ligand.  
     
     
         73 . The method of  claim 60 , wherein the composition further comprises a binding enhancer that has a specific affinity for nucleic acids.  
     
     
         74 . The method of  claim 73 , wherein the binding enhancer is an intercalator or a non-intercalator.  
     
     
         75 . The method of  claim 73 , wherein the binding enhancer has an affinity for nucleic acids equal to or greater than 1×10 4  mole −1 , specifically binds to nucleic acids in the presence of greater than 10 mM magnesium or comprises a nucleotide sequence that specifically binds to a target nucleic acid to be analyzed.  
     
     
         76 . The method of  claim 60 , wherein the composition further comprises a lysing reagent for releasing a target nucleic acid to be analyzed.  
     
     
         77 . The method of  claim 73 , wherein the binding ligand, binding enhancer and signature label in at least one of the compositions are bound together in the form of a covalent or noncovalent complex.  
     
     
         78 . The method of  claim 59 , further comprising hybridizing the target nucleic acid to a complementary probe.  
     
     
         79 . The method of  claim 59 , wherein the photoactivatable label not attached to the target nucleic acid is removed or inactivated prior to or concurrently with analyzing the label attached to the target nucleic acid.  
     
     
         80 . The method of  claim 59 , wherein a plurality of target nucleic acids is quantified simultaneously.  
     
     
         81 . The method of  claim 1 , wherein the labeled target nucleic acids are hybridized to a plurality of probes and each of said probes hybridizes to a different kind of target nucleic acid.  
     
     
         82 . The method of claim Si, wherein the labeled target nucleic acids are hybridized to the plurality of probes simultaneously.  
     
     
         83 . The method of  claim 1 , wherein the labeled target nucleic acids are comprise DNA, RNA, PNA or a combination thereof.  
     
     
         84 . The method of  claim 80 , further comprising hybridizing the target nucleic acid to a complementary probe and wherein the plurality of target nucleic acids is hybridized to a plurality of probes and each of said probes hybridizes to a different kind of target nucleic acid.  
     
     
         85 . The method of  claim 1 , wherein the chemiluminescent compound is an acridinium ester.