Closed-system multi-stage nucleic acid amplification reactions

• US 8,133,703 B2
• Filed: 10/27/2005
• Issued: 03/13/2012
• Est. Priority Date: 10/27/2004
• Status: Active Grant

• Current Assignee: Cepheid (Danaher Corporation)
• Original Assignee: Ceoheid
• Inventors: Ching, Jesus, Chang, Ronald, Dority, Douglas Bryan, Zhang, Jian Ping, Wang, James Jian Quan, Wong, Wendy Wingkei, Paul, Kendra Lara, Van Atta, Reuel
• Primary Examiner(s): Strzelecka, Teresa E
• Assistant Examiner(s): Pande, Suchira
• Application Number:
  US11/262,523
• Publication Number:
  US 20060177844A1
• Time in Patent Office: 2,329 Days
• Field of Search: None
• US Class Current: 435/91.2
• CPC Class Codes: B01L 2200/0684 Venting, avoiding backpressure, avoid gas bubbles
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2300/0877 Flow chambers
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0644 rotary valves
• CPC Class Codes: B01L 3/502 with fluid transport, e.g. in multi-compartment structures centrifugal-type cuvettes G01N21/07; analysis by separation into components G01N30/00; automatic analysers G01N35/00
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2531/143 Promoter based amplification, e.g. NASBA, 3SR, TAS
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2549/119 using nested primers
• CPC Class Codes: C12Q 2563/173 staining/intercalating agent, e.g. ethidium bromide
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53

Abstract

The invention is directed to systems, methods, and apparatus for carrying out multi-stage amplification reactions, especially under fluidly closed conditions. In one aspect, methods of the invention are carried out in a fluidly closed reaction system that permits the isolation of a portion of a first (or prior) reaction mixture and its use as a sample or specimen in a second (or subsequent) reaction mixture, thereby substantially avoiding interfering effects that first reaction components may have in the second reaction if both reaction mixtures were simply combined together. In this aspect, systems, methods, and apparatus of the invention may be used with any amplification reaction that permits multiple stages of amplification based on the use of nested primers.

Claims

1. A method of controlling a nested amplification reaction, the method comprising the steps of:

a) amplifying in a reaction chamber of a fluidly closed system, a first-stage amplification reaction comprising one or more target polynucleotides from a sample using first-stage amplification reagents in a first reaction mixture to form one or more first amplicons, the first-stage amplification reagents including initial primers for each target polynucleotide, wherein the one or more first amplicons are amplified in the presence of a fluorescent indicator capable of generating an optical signal related to a quantity of an amplicon in the first-stage amplification reaction,

the reaction chamber comprising a retaining member positioned in the reaction chamber to retain a defined volume of the liquid in the reaction chamber whenever the remainder of the liquid is removed from the reaction chamber;

b) monitoring the optical signal of the fluorescent indicator in the first-stage amplification reaction in the reaction chamber;

c) automatically withholding by the retaining member in the reaction chamber an effective portion of the reaction mixture of the first-stage amplification reaction when the optical signal reaches or exceeds a threshold level;

d) amplifying in the reaction chamber the one or more first amplicons in the effective portion using second-stage amplification reagents in a second reaction mixture to form one or more second amplicons, the second-stage amplification reagents including at least one secondary primer for each of the one or more first amplicons, such that each secondary primer is nested in such first amplicon relative to an initial primer of such first amplicon; and

e) detecting the one or more second amplicons to determine the presence or absence of the one or more target polynucleotides in the sample.

2. The method of claim 1 wherein said reaction mixture of said first-stage amplification reaction is in the reaction chamber of the fluidly closed reaction system and wherein said step of automatically separating includes fluidly transferring said first-stage reaction mixture to a waste reservoir, except for the effective portion that remains in the reaction chamber.

3. The method of claim 2 wherein said effective portion is a volume of said reaction mixture sufficient to contain at least one molecule of said one or more first amplicons.

4. The method of claim 3 wherein said effective portion is a volume of said reaction mixture sufficient to contain at least 100 molecules of said one or more first amplicons.

5. The method of claim 2 wherein said reaction mixture has a volume and wherein said effective portion is a percentage of the volume of said reaction mixture, the percentage being selected from the range of 0.5 to 10 percent.

6. The method of claim 1 wherein said threshold level is a multiple of a baseline signal level, the multiple being selected from the range of 1.5 to 25.

7. The method of claim 1 wherein said threshold level corresponds to a maximum, minimum, or zero-value of a growth curve defined by the optical signal.

8. The method of claim 1 wherein said fluorescent indicator is an intercalating dye that specifically binds to double stranded DNA or comprises an oligonucleotide moiety that specifically binds to an amplification product.

9. The method of claim 1 wherein said one or more first amplicons is produced by amplification of a reference sequence in said first-stage amplification reaction.

10. The method of claim 1 wherein said one or more first amplicons is produced by amplification of a target polynucleotide in said first-stage amplification reaction.

11. The method of claim 1 wherein said fluidly closed reaction system comprises:

a reaction chamber selectably in fluid communication with a sample reservoir containing said sample, a first reactant reservoir containing the first-stage amplification reagents, and a second reactant reservoir containing the second-stage amplification reagents, each of said reservoirs being fluidly closed.

12. A method of detecting the presence or absence of one or more target polynucleotides in a sample, the method comprising the steps of:

providing a fluidly closed system comprising a reaction chamber selectably in fluid communication with a waste reservoir, a sample reservoir containing a sample, a first reactant reservoir containing first-stage amplification reagents, and a second reactant reservoir containing second-stage amplification reagents;

the reaction chamber comprising a retaining member positioned in the reaction chamber to retain a defined volume of the liquid in the reaction chamber whenever the remainder of the liquid is removed from the reaction chamber;

fluidly transferring sample from the sample reservoir and first-stage amplification reagents from the first reactant reservoir to the reaction chamber so that the first-stage amplification reagents react with the sample in a first stage amplification reaction in the reaction chamber to produce a reaction product containing a first amplicon whenever a target polynucleotide is present in the sample;

optically monitoring a fluorescent indicator in the first stage amplification reaction in the reaction chamber;

fluidly transferring the reaction product to the waste reservoir, except for an effective portion withheld by the retaining member in the reaction chamber, when the optical signal reaches or exceeds a threshold level;

fluidly transferring second-stage amplification reagents from the second reactant reservoir to the reaction chamber so that the second-stage amplification reagents react with the effective portion of the reaction product in a second amplification reaction in the reaction chamber to produce a second amplicon whenever the first amplicon is present in the reaction product; and

detecting the second amplicon to determine whether the target polynucleotide is present in the sample.

13. The method of claim 12 wherein said amplification reaction with said first-stage amplification reagents is a polymerase chain reaction performed for a predetermined number of cycles, and wherein said step of fluidly transferring said reaction product is implemented after the predetermined number of cycles of said amplification reaction.

14. The method of claim 13 wherein said predetermined number of cycles in said amplification reaction is in the range of from 20 to 50.

15. The method of claim 12 wherein said step of fluidly transferring said reaction product includes the steps of monitoring an optical signal from a fluorescent indicator associated with said first amplicon, the optical signal being monotonically related to the quantity of said first amplicon;

and automatically separating said effective portion of said reaction product whenever the optical signal is equal to or greater than a predetermined level.

16. The method of claim 15 wherein said reaction product has a volume and wherein said effective portion is a percentage of the volume of said reaction product, the percentage being selected from the range of 0.5 to 10 percent.

17. The method of claim 16 wherein said predetermined level is a multiple of a baseline signal level, the multiple being selected from the range of 1.5 to 25.

18. The method of claim 16 wherein said amplification reactions are each a polymerase chain reaction or a NASBA reaction.

19. The method of claim 18 wherein said fluorescent indicator is an intercalating dye that specifically binds to double stranded DNA or comprises an oligonucleotide moiety that specifically binds to an amplification product.

20. A method of amplifying one or more RNA sequences, the method comprising the steps of:

transcribing one or more RNA sequences in a fluidly closed reaction system to form one or more complementary single stranded DNA sequences using reverse transcriptase reagents in a first reaction mixture;

optically monitoring a fluorescent indicator in the first stage amplification reaction

isolating a first effective portion of the first reaction mixture in the fluidly closed reaction system, wherein said first reaction mixture is in a reaction chamber of said fluidly closed reaction system, the reaction chamber comprising a retaining member positioned in the reaction chamber to retain a defined volume of the liquid in the reaction chamber whenever the remainder of the liquid is removed from the reaction chamber, and wherein said step of isolating said first effective portion includes fluidly transferring said first reaction mixture to a waste reservoir, except for said first effective portion that is withheld by the retaining member in the reaction chamber, when the optical signal in the reaction chamber reaches or exceeds a threshold level; and

amplifying in the reaction chamber the one or more complementary single stranded DNA sequences in the first effective portion using first-stage amplification reagents in a second reaction mixture to form one or more first amplicons, the first-stage amplification reagents including initial primers for each of the complementary single stranded DNA sequences.

21. The method of claim 20 wherein said reaction chamber has a bottom and an outlet port positioned above the bottom so that whenever said first-stage reaction mixture is fluidly transferred to said waste reservoir through the outlet port a retained volume of said first-stage reaction mixture is retained in said reaction chamber below the outlet port, wherein the retained volume comprises said first effective portion.

22. The method of claim 20 wherein said first reaction mixture has a volume and wherein said effective portion is a percentage of the volume of said first reaction mixture, the percentage being selected from the range of from 0.5 to 20 percent.

23. The method of claim 22 further including the steps of:

isolating a second effective portion of said second reaction mixture in said fluidly closed reaction system;

amplifying in said fluidly closed reaction system said one or more first amplicons in said second effective portion using second-stage amplification reagents in a third reaction mixture to form one or more second amplicons, the second-stage amplification reagents including at least one secondary primer for each of the one or more first amplicons, such that each secondary primer is nested in such first amplicon relative to said initial primer of such first amplicon.

24. The method of claim 23 wherein said second reaction mixture is in said reaction chamber of said fluidly closed reaction system and wherein said step of isolating said second effective portion includes fluidly transferring said second reaction mixture to said waste reservoir, except for said second effective portion that remains in said reaction chamber.

25. A method for detecting the presence or absence of one or more target polynucleotides in a sample, the method comprising the steps of:

providing a reaction chamber containing first-stage amplification reagents, the reaction chamber being selectably in fluid communication with a waste reservoir, a sample reservoir containing a sample, and a second reactant reservoir containing second-stage amplification reagents, each of said reservoirs being fluidly closed;

the reaction chamber comprising a retaining member positioned in the reaction chamber to retain a defined volume of the liquid, as an effective portion, in the reaction chamber whenever the remainder of the liquid is removed from the reaction chamber;

fluidly transferring sample from the sample reservoir to the reaction chamber so that the first-stage amplification reagents react with the sample in a first stage amplification reaction in the reaction chamber to produce a first reaction product containing a first amplicon if a target polynucleotide is present in the sample;

optically monitoring a fluorescent indicator in the first stage amplification reaction in the reaction chamber;

fluidly transferring the first reaction product to the waste reservoir, except for the an effective portion of the first reaction product withheld by the retaining member in the reaction chamber, when the optical signal reaches or exceeds a threshold level;

fluidly transferring the second-stage amplification reagents from the second reactant reservoir to the reaction chamber so that the second-stage amplification reagents react with the effective portion of the first reaction product in a second stage amplification reaction in the reaction chamber to produce a second amplicon whenever the first amplicon is present in the first reaction product; and

detecting the second amplicon to determine whether the target polynucleotide is present in the sample.