Method for determining the amount of template nucleic acid present in a sample

• US 8,309,308 B2
• Filed: 07/29/2005
• Issued: 11/13/2012
• Est. Priority Date: 07/29/2004
• Status: Active Grant

• Current Assignee: Lumora Ltd. (Transasia Bio-Medicals Ltd.)
• Original Assignee: Lumora Ltd. (Transasia Bio-Medicals Ltd.)
• Inventors: Tisi, Laurence Carlo, Murray, James Augustus Henry, Gandelman, Olga, Church, Victoria Louise
• Primary Examiner(s): Chunduru, Suryaprabha
• Application Number:
  US11/632,639
• Publication Number:
  US 20080118921A1
• Time in Patent Office: 2,664 Days
• Field of Search: 435/6, 435/91.2, 536/24.33
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)

Abstract

A method for determining the amount of template nucleic acid present in a sample comprising the steps of: i) bringing into association with the sample all the components necessary for nucleic acid amplification, and all the components necessary for a bioluminescence assay for nucleic acid amplification and subsequently: ii) performing the nucleic acid amplification reaction; iii) monitoring the intensity of light output from the bioluminescence assay; and iv) determining the amount of template nucleic acid present in the sample.

Claims

1. A method for determining the amount of template nucleic acid present in a sample comprising the steps of:

i) bringing into association with the sample all the components necessary for nucleic acid amplification, and all the components necessary for a bioluminescence assay for nucleic acid amplification including;

a) a nucleic acid polymerase,

b) the substrates for the nucleic acid polymerase,

c) at least two primers,

d) a thermostable luciferase,

e) luciferin,

f) an enzyme that converts PPi to ATP, wherein the enzyme is not ATP sulphurylase, and

any other required substrates or cofactors of the enzyme of part f), wherein the substrate or cofactor is not PPi,

wherein when the enzyme of part f) is pyruvate orthophosphate dikinase, the substrates added in part g) are phosphoenolpyruvate and AMP; and

subsequently;

ii) performing a nucleic acid amplification reaction of the template nucleic acid, wherein generated copies are themselves further copied;

iii) coupling the production of PPi to light output from the bioluminescence assay by converting generated PPi to ATP and using luciferase to follow the changes in the concentration of ATP by monitoring the intensity of light output from the bioluminescence reaction; and

iv) determining the amount of template nucleic acid present in the sample.

2. A method according to claim 1, wherein at least steps ii) and iii) are carried out in a sealed vessel.

3. A method according to claim 1, wherein in step iii) the intensity of light output is monitored during the nucleic acid amplification reaction.

4. A method according to claim 1, wherein step iii) further includes producing a data set of intensity of light output as a function of time.

5. A method according to claim 4, wherein the amount of template nucleic acid present is determined by measuring from the data set the time taken to reach a point at which the rate of change of intensity of light output changes significantly.

6. A method according to claim 1 for determining the amount of template nucleic acid present in the sample at the beginning of the nucleic acid amplification reaction of step ii).

7. A method according to claim 1 for determining the amount of template nucleic acid present in the sample as a result of the nucleic acid amplification reaction of step ii).

8. A method according to claim 5, wherein the amount of template nucleic acid present is determined by measuring from the data set the time taken to reach a point at which the intensity of light output begins to increase.

9. A method according to claim 5, wherein the amount of template nucleic acid present is determined by measuring from the data set the time taken to reach a point at which the intensity of light output is at a maximum.

10. A method according to claim 5, wherein the amount of template nucleic acid present is determined by measuring from the data set the time taken to reach a point at which the rate of decrease of intensity of light output increases.

11. A method according to claim 5, wherein the amount of template nucleic acid present is determined by measuring from the data set the time taken to reach a point at which the rate of decrease of intensity of light output decreases.

12. A method according to claim 5, wherein the amount of template nucleic acid present is determined by measuring from the data set the time taken to reach a point at which the intensity of light output reaches or crosses a predetermined level.

13. A method according to claim 1, wherein step iv) further comprises comparing the intensity of light output to the intensity of light output from a control in which the sample comprises a known amount of template nucleic acid.

14. A method according to claim 1 for determining whether the template nucleic acid is present in the sample.

15. A method according to claim 14, wherein whether the template nucleic acid is present in the sample is determined by measuring from the data set whether the intensity of light output reaches or crosses a predetermined level.

16. A method according to claim 15, wherein an increase in the intensity of light output relative to the predetermined level indicates the presence of template nucleic acid in the sample.

17. A method according to claim 15, wherein a decrease in the intensity of light output relative to the predetermined level indicates the presence of template nucleic acid in the sample.

18. A method according to claim 15, wherein whether the template nucleic acid is present in the sample is determined by measuring from the data set whether the intensity of light output reaches or crosses the predetermined level within a predetermined length of time following the start of the amplification reaction of step ii).

19. A method according to claim 1, wherein step iv) further comprises comparing the intensity of light output to the intensity of light output from a control in which no amplification has taken place.

20. A method according to claim 19, wherein a decrease in the intensity of light output relative to a control reaction in which no amplification has taken place indicates the presence of template nucleic acid in the sample.

21. A method according to claim 1, wherein the nucleic acid amplification reaction of step ii) is a low temperature thermocycling amplification method in which the cycling temperature range does not exceed 75°

C.

22. A method according to claim 1, wherein the nucleic acid amplification reaction of step ii) is carried out isothermally.

23. A method according to claim 22, wherein the nucleic acid amplification reaction of step ii) is carried out within a temperature range that does not exceed 75°

C.

24. A method according to claim 22, wherein the nucleic acid amplification reaction of step ii) is carried out at a constant temperature at which the components of the amplification reaction and the bioluminescence assay are stable.

25. A method according to claim 22, wherein the nucleic acid amplification reaction of step ii) is carried out at more than one temperature within the temperature range in which the components of the amplification reaction and the bioluminescence assay are stable.

26. A method according to claim 25, wherein the nucleic acid amplification reaction of step ii) is started at a higher temperature and subsequently dropped to a lower temperature.

27. A method according to claim 1 for use in medical diagnostics.

28. A method according to claim 1 for use in determining whether a pathogen is present in a sample.

29. A method according to claim 1 for determining whether a particular nucleic acid sequence is present in an organism'"'"'s genetic code.

30. A method according to claim 29 for determining whether the nucleic acid to which the template nucleic acid originates has been genetically modified.

31. A method according to claim 1 for determining whether an organism is present in a sample.

32. A method according to claim 1 for use in immuno-nucleic acid amplification technology.

33. A method according to claim 31, for determining whether Chlamydia trachomatis is present in a sample.

34. A method according to claim 1, wherein the enzyme that converts PPi to ATP is pyruvate orthophosphate dikinase (PPDK) and the substrates of the enzyme are phosphoenylpyruvate and AMP, wherein in step iii) the intensity of light output is monitored during the nucleic acid amplification reaction, and wherein step iii) further includes producing a data set of intensity of light output as a function of time.

37. A method according to claim 1, wherein when the enzyme of part f) is nicotinamide-mononucleotide adenylyltransferase, the cofactor added in part g) is NAD⁺.

38. A method according to claim 1, wherein when the enzyme of part f) is ATP diphosphatase, the substrate added in part g) is AMP.

39. A method according to claim 1, wherein when the enzyme of part f) is ATP phosphoribosyltransferase, the substrate added in part g) is 1-(5-phospho-D-ribosyl)-ATP.

35. A method for determining the amount of template nucleic acid present in a sample comprising the steps of:

i) bringing into association with the sample all components necessary for a nucleic acid amplification reaction, which releases pyrophosphate (PPi) for each nucleotide incorporated into a growing chain of nucleotides, and all components necessary for a bioluminescence assay, which converts PPi into ATP, including;

a) a nucleic acid polymerase,

b) substrates for the nucleic acid polymerase,

c) at least two primers,

d) a thermostable luciferase,

e) luciferin,

f) an enzyme that converts PPi to ATP which is neither ATP sulphurylase nor pyruvate orthophosphate dikinase, and

g) any other required substrates or cofactors of the enzyme of part f) which is not PPi;

and subsequently;

ii) performing the nucleic acid amplification reaction of the template nucleic acid, which generates copies of the template nucleic acid that are themselves further copied, coupled to the bioluminescence assay for quantitating PPi produced as a consequence of nucleic acid polymerization;

iii) monitoring the light output from the bioluminescence assay; and

iv) determining the amount of template nucleic acid present in the sample from the light output.

36. A method according to claim 35, wherein the enzyme of part f) is selected from the group consisting of nicotinamide-mononucleotide adenylyltransferase, ATP diphosphatase, and ATP phosphoribosyltransferase.