Methods of nonspecific target capture of nucleic acids

Abstract

Methods for capturing a target nucleic acid from a sample by using a capture probe that binds nonspecifically to the target nucleic acid and binds specifically to an immobilized probe via a specific binding pair that has one member on the capture probe and one member on the immobilized probe are disclosed. Compositions that include a capture probe that binds nonspecifically to a target nucleic acid and specifically to an immobilized probe via binding of members of a specific binding pair in a solution phase of a reaction mixture are disclosed.

We claim: 
     
         1 . A method for isolating a target DNA from a sample, said method comprising:
 1) mixing a sample containing the target DNA in a solution phase with a non-specific capture probe, wherein said non-specific capture probe comprises
 (i) a randomized poly-(k) sequence that is at least 12 residues in length and comprising G and T nucleotides or G and U nucleotides, or a nonrandom repeating (GU) sequence that is at least 12 residues in length, and 
 (ii) a first specific binding partner (SBP), wherein said SBP is capable of specifically binding a second specific binding partner (SBP′); 
   2) incubating a reaction mixture containing (a) the SBP′ immobilized on a support and (b) the mixture of the non-specific capture probe and the sample containing the target DNA, wherein said incubating is under conditions that allow hybridization of the capture probe's poly-(k) sequence with the target DNA and that allow specific binding of the SBP to the SBP′; and   3) separating the support from the solution phase of the reaction mixture, thereby isolating the target DNA from other sample components.   
     
     
         2 . The method of  claim 1 , wherein the sample contains cells and is treated before the mixing step to release intracellular components into the solution phase. 
     
     
         3 . The method of  claim 2 , wherein said treatment comprises treating the sample with a solution containing a detergent. 
     
     
         4 . The method of  claim 2 , wherein the sample comprises peripheral blood. 
     
     
         5 . The method of  claim 1 , wherein the poly-(k) sequence comprises G and U nucleotides. 
     
     
         6 . The method of  claim 5 , wherein the poly-(k) sequence comprises 2′-O-methyl substituted RNA bases, or wherein the nonrandom repeating (GU) sequence comprises 2′-O-methyl substituted RNA bases. 
     
     
         7 . The method of  claim 1 , wherein the poly-(k) sequence is a poly-(k) 18 , poly-(k) 24 , or poly-(k) 25  sequence. 
     
     
         8 . The method of  claim 1 , wherein the SBP and SBP′ are non-nucleic acid moieties. 
     
     
         9 . The method of  claim 1 , wherein the SBP and SBP′ are substantially complementary nucleic acid sequences. 
     
     
         10 . The method of  claim 9 , wherein the SBP is situated 3′ to the poly-(k) sequence. 
     
     
         11 . The method of  claim 9 , wherein the SBP is a dT 3 dA 30  or dA 30  sequence. 
     
     
         12 . The method of  claim 1 , wherein the solution phase comprises a detergent. 
     
     
         13 . The method of  claim 1 , wherein the solution phase comprises lithium lauryl sulfate and lithium hydroxide. 
     
     
         14 . The method of  claim 1 , further comprising detecting the presence of the target DNA isolated from other sample components, amplifying in vitro a sequence contained in the target DNA isolated from other sample components, or determining a sequence contained the target DNA isolated from other sample components. 
     
     
         15 . A method for isolating a target DNA from a peripheral blood sample, said method comprising:
 1) treating a peripheral blood sample containing the target DNA to release intracellular components into a solution phase;   2) mixing the treated sample containing the target DNA in the solution phase with a non-specific capture probe, wherein said non-specific capture probe comprises
 (i) a randomized poly-(k) 18  sequence comprising G and U nucleotides with 2′-methoxy substituted RNA bases, and 
 (ii) a first specific binding partner (SBP), wherein said SBP is capable of specifically binding a second specific binding partner (SBP′); 
   3) incubating a reaction mixture containing (a) the SBP′ immobilized on a support and (b) the mixture of the non-specific capture probe and the treated sample containing the target DNA, wherein said incubating is under conditions that allow hybridization of the capture probe's poly-(k) sequence with the target DNA and that allow specific binding of the SBP to the SBP′; and   4) separating the support from the solution phase of the reaction mixture, thereby isolating the target DNA from other peripheral blood sample components.   
     
     
         16 . A method for isolating a target DNA from a sample, said method comprising:
 1) mixing a sample containing the target DNA in a solution phase with a non-specific capture probe, wherein said sample is provided as a lysate made from cells comprising the target DNA, and wherein said non-specific capture probe comprises
 (i) a randomized poly-(k) sequence that is at least 12 residues in length and comprising G and T nucleotides or G and U nucleotides, and 
 (ii) a first specific binding partner (SBP), wherein said SBP is capable of specifically binding a second specific binding partner (SBP′); 
   2) incubating a reaction mixture containing (a) the SBP′ immobilized on a support and (b) the mixture of the non-specific capture probe and the sample containing the target DNA, wherein said incubating is under conditions that allow hybridization of the capture probe's poly-(k) sequence with the target DNA and that allow specific binding of the SBP to the SBP′; and   3) separating the support from the solution phase of the reaction mixture, thereby isolating the target DNA from other sample components.   
     
     
         17 . The method of  claim 16 , wherein the sample comprises peripheral blood. 
     
     
         18 . The method of  claim 16 , wherein the poly-(k) sequence comprises G and U nucleotides. 
     
     
         19 . The method of  claim 18 , wherein the poly-(k) sequence comprises 2′-O-methyl substituted RNA bases. 
     
     
         20 . The method of  claim 16 , wherein the poly-(k) sequence is a poly-(k) 18 , poly - (k) 24 , or poly-(k) 25  sequence. 
     
     
         21 . The method of  claim 16 , wherein the SBP and SBP′ are non-nucleic acid moieties. 
     
     
         22 . The method of  claim 16 , wherein the SBP and SBP′ are substantially complementary nucleic acid sequences. 
     
     
         23 . The method of  claim 22 , wherein the SBP is situated 3′ to the poly-(k) sequence. 
     
     
         24 . The method of  claim 22 , wherein the SBP is a dT 3 dA 30  or dA 30  sequence. 
     
     
         25 . The method of  claim 16 , wherein the solution phase comprises a detergent. 
     
     
         26 . The method of  claim 16 , further comprising detecting the presence of the target DNA isolated from other sample components, amplifying in vitro a sequence contained in the target DNA isolated from other sample components, or determining a sequence contained the target DNA isolated from other sample components. 
     
     
         27 . A reaction mixture for isolating a target DNA from a sample, said reaction mixture comprising:
 a) a sample containing the target DNA in a solution phase;   b) a non-specific capture probe, wherein said non-specific capture probe comprises
 (i) a randomized poly-(k) sequence that is at least 12 residues in length and comprising G and T nucleotides or G and U nucleotides, and 
 (ii) a first specific binding partner (SBP), wherein said SBP is capable of specifically binding a second specific binding partner (SBP′); and 
   c) the SBP′ immobilized on a support.   
     
     
         28 . The reaction mixture of  claim 27 , wherein the sample is derived from cells that have been treated to release intracellular components into the solution phase. 
     
     
         29 . The reaction mixture of  claim 28 , wherein the solution phase comprises a detergent used in said treatment. 
     
     
         30 . The reaction mixture of  claim 28 , wherein the sample comprises peripheral blood. 
     
     
         31 . The reaction mixture of  claim 27 , wherein the poly-(k) sequence comprises G and U nucleotides. 
     
     
         32 . The reaction mixture of  claim 31 , wherein the poly-(k) sequence comprises 2′-O-methyl substituted RNA bases. 
     
     
         33 . The reaction mixture of  claim 27 , wherein the poly-(k) sequence is a poly-(k) 18 , poly-(k) 24 , or poly-(k) 25  sequence. 
     
     
         34 . The reaction mixture of  claim 27 , wherein the SBP and SBP′ are non-nucleic acid moieties. 
     
     
         35 . The reaction mixture of  claim 27 , wherein the SBP and SBP′ are substantially complementary nucleic acid sequences. 
     
     
         36 . The reaction mixture of  claim 35 , wherein the SBP is situated 3′ to the poly-(k) sequence. 
     
     
         37 . The reaction mixture of  claim 35 , wherein the SBP is a dT 3 dA 30  or dA 30  sequence. 
     
     
         38 . The reaction mixture of  claim 27 , wherein the solution phase comprises a detergent. 
     
     
         39 . The reaction mixture of  claim 27 , wherein the solution phase comprises lithium lauryl sulfate and lithium hydroxide.