Method for detecting the presence of a nucleic acid in a sample

Abstract

An automated method for detecting the presence of a nucleic acid in a sample, where the method is performed within a housing of a self-contained, stand-alone analyzer. The method includes purifying the nucleic acid after it has been immobilized on a magnetically-responsive solid support. A pipette of the analyzer is used to form a reaction mixture comprising the purified nucleic acid and all reagents required to perform a nucleic acid amplification. Amplification products are synthesized that include a nucleotide sequence contained in the nucleic acid or the complement of the nucleic acid. The amplification products are exposed to a probe in a mixture, where the probe forms a hybrid with one of the amplification products. The formation of the hybrid in the mixture provides an indication of the presence of the nucleic acid in the sample.

1 . (canceled) 
     
     
         2 . A method for detecting the presence of a nucleic acid in a sample, the method comprising performing within a housing of a self-contained, stand-alone analyzer the automated steps of:
 a) contacting the sample with a solid support such that a complex comprising the nucleic acid and the solid support is formed in the sample, wherein the solid support comprises a magnetically-responsive particle, and wherein the complex is suspended in a fluid component of the sample;   b) after step a), moving one or more permanent magnets of the analzyer from a down position to an up position relative to the sample, such that the sample is subjected to at least one magnetic field when the one or more magnets are in the up position, wherein the one or more magnets have no substantial effect on the solid support when the one or more magnets are in the down position;   c) while the sample is subjected to the at least one magnetic field, aspirating at least a portion of the fluid component of the sample from the complex;   d) after step c), washing the solid support one or more times with a wash buffer, thereby providing a purified form of the nucleic acid;   e) forming a reaction mixture with a pipette assembly, wherein the reaction mixture comprises the purified form of the nucleic acid and all reagents required to perform a nucleic acid amplification;   f) synthesizing amplification products in the reaction mixture, each of the amplification products comprising a nucleotide sequence contained in the nucleic acid or its complement;   g) exposing an amplification product that is one of the amplification products synthesized in step f) to a probe having a label, such that a hybrid comprising the probe and the amplification product is formed in solution in a mixture containing the probe and the amplification products; and   h) in the mixture of step g), detecting the label after formation of the hybrid, wherein the formation of the hybrid in the mixture is an indication of the presence of the nucleic acid in the sample.   
     
     
         3 . The method of  claim 2 , further comprising, prior to step a), a manual step of providing the sample and the reagents to the analyzer, wherein the sample and the reagents are separately provided to the analyzer. 
     
     
         4 . The method of  claim 2 , wherein the complex formed in step a) further comprises a capture probe hybridized to the nucleic acid. 
     
     
         5 . The method of  claim 2 , wherein the one or more magnets pivot between the down position and the up position during step b). 
     
     
         6 . The method of  claim 2 , wherein the portion of the fluid component of the sample aspirated in step c) is aspirated from a receptacle having an open top end and a closed bottom end. 
     
     
         7 . The method of  claim 2 , wherein the fluid component is aspirated through a tiplet in frictional engagement with an aspirator tube of a fluid aspirator of the analyzer. 
     
     
         8 . The method of  claim 2 , further comprising, prior to step c), an automated step of sensing the level of the fluid component. 
     
     
         9 . The method of  claim 2 , wherein the portion of the fluid component aspirated in step c) is drawn through an aspirator tube to a fluid waste container. 
     
     
         10 . The method of  claim 9 , wherein the fluid waste container is situated in a lower chassis of the analyzer beneath a processing deck contained within the housing. 
     
     
         11 . The method of  claim 2 , wherein the steps of the method are performed in a single receptacle. 
     
     
         12 . The method  claim 11 , wherein the receptacle is open-ended when performing the steps of the method. 
     
     
         13 . The method of  claim 11 , wherein the receptacle is a cylindrical tube. 
     
     
         14 . The method of  claim 11 , wherein the receptacle is one of a plurality of integrally formed receptacles. 
     
     
         15 . The method of  claim 2 , wherein the amplification products formed in step f) comprise amplification products having the nucleotide sequence contained in the nucleic acid and amplification products having the nucleotide sequence contained in the complement of the nucleic acid. 
     
     
         16 . The method of  claim 2 , wherein the probe hybridizes with specificity to the amplification product in step g), and wherein the nucleic acid is from a disease-associated pathogen. 
     
     
         17 . The method of  claim 2 , wherein the label is a fluorescent or chemiluminescent label. 
     
     
         18 . The method of  claim 2 , wherein step f) is performed within an enclosure having a receptacle access opening, the receptacle access opening being closed by a door of the enclosure during step f). 
     
     
         19 . The method of  claim 2 , wherein the analyzer is controlled by a computer controller that is integrally housed within the analyzer. 
     
     
         20 . The method of  claim 2 , wherein the steps of the method are performed at multiple stations situated on a processing deck contained within the housing. 
     
     
         21 . The method of  claim 2 , wherein the housing remains closed when performing the steps of the method.