Methods for capture and selective release of nucleic acids using weakly basic polymer and amplification of same

• US 5,582,988 A
• Filed: 09/15/1994
• Issued: 12/10/1996
• Est. Priority Date: 09/15/1994
• Status: Expired due to Term

• Current Assignee: Clinical Diagnostic Systems Inc.
• Original Assignee: Johnson & Johnson Clinical Diagnostics Inc. (Johnson & Johnson)
• Inventors: Findlay, John B., Backus, John W., Kerschner, JoAnne H., Sutton, Richard C., Ponticello, Ignazio S., Ekeze, Tobias E., Swartz, Jerome C.
• Primary Examiner(s): Zitomer, Stephanie W.
• Assistant Examiner(s): CAMPBELL, EGGERTON A
• Application Number:
  US08/306,870
• Time in Patent Office: 817 Days
• Field of Search: 435/6, 435/5, 536/23.1
• US Class Current: 435/6.12
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C07K 14/35 from Mycobacteriaceae (F)
• CPC Class Codes: C08F 20/34 Esters containing nitrogen , e.g. N,N-dimethylaminoethyl (meth)acrylate
• CPC Class Codes: C08F 20/60 containing nitrogen in addition to the carbonamido nitrogen
• CPC Class Codes: C12N 15/1003 Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
• CPC Class Codes: C12N 15/1006 by means of a solid support carrier, e.g. particles, polymers
• CPC Class Codes: C12N 2710/16122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 2740/16022 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence

Abstract

Nucleic acids can be made available for amplification or other treatment after lysis by contacting the lysate with specific weakly basic polymers to form a precipitate with the nucleic acids at acidic pH. After removing non-precipitated materials, the pH is then made basic, thereby releasing the nucleic acids from the polymer. This method for preparing specimen samples is simple and quite rapid, and the released nucleic acids can be further treated in hybridization assays or amplification procedures. The weakly basic polymers are water-soluble and cationic at acidic pH, but neutral in charge at basic pH.

Claims

1. A method for providing a nucleic acid from a lysate comprising the steps of:

A) at a pH of less than 7, contacting a lysate suspected of containing a nucleic acid with a water-soluble, weakly basic polymer comprised of recurring units derived by addition polymerization of;

1) from about 15 to 100 weight percent of a water-soluble, weakly basic ethylenically unsaturated polymerizable monomer having at least one group which can be protonated at acidic pH and which is selected from the group consisting of aminoalkyl, imidazolyl, isoxazolyl, pyridyl, piperidyl, piperazinyl, pyrazolyl, triazolyl, tetrazolyl, oxadiazolyl, pryidazinyl, pyrimidyl, pyrazinyl, quinolinyl and quinazolinyl,

2) from 0 to about 35 weight percent of a nonionic, hydrophilic ethylenically unsaturated polymerizable monomer, and

3) from 0 to about 85 weight percent of a nonionic, hydrophobic ethylenically unsaturated polymerizable monomer in an amount sufficient to form a water-insoluble precipitate of said weakly basic polymer with all nucleic acids present in said lysate,

B) separating said water-insoluble precipitate from said lysate, and

C) contacting said precipitate with a base to raise the solution pH to greater than 7, and thereby releasing said nucleic acids from said weakly basic polymer,

said weakly basic polymer comprising recurring units derived by addition polymerization of one or more ethylenically unsaturated polymerizable monomers having an amine group which can be protonated at acidic pH.

2. The method of claim 1 further comprising the step:

D) adjusting the pH of said solution containing said released nucleic acids to from about 6 to about 9.

3. The method of claim 1 wherein said base is sodium hydroxide, potassium hydroxide, ammonium hydroxide, lithium hydroxide, sodium carbonate, sodium bicarbonate, a tertiary amine or tris(hydroxymethyl)-aminomethane.

4. The method of claim 1 wherein said weakly basic polymer is used in step A) in an amount of from about 0.01 to about 0.5 weight %.

5. The method of claim 1 wherein a weak base is used in step C), accompanied by heating said water-insoluble precipitate at from about 50°

to about 125°

C.

6. The method of claim 1 wherein a strong base is used in step C) without heating said water-insoluble precipitate.

7. A method for the amplification and detection of a target nucleic acid comprising:

I) providing a target nucleic acid using the steps of;

A) at a pH of less than 7, contacting a lysate suspected of containing a target nucleic acid with a water-soluble, weakly basic polymer comprised of recurring units derived by addition polymerization of;

1) from about 15 to 100 weight percent of a water-soluble, weakly basic ethylenically unsaturated polymerizable monomer having at least one group which can be protonated at acidic pH and which is selected from the group consisting of aminoalkyl, imidazolyl, isoxazolyl, pyridyl, piperidyl, piperazinyl, pyrazolyl, triazolyl, tetrazolyl, oxadiazolyl, pyridazinyl, pyrimidyl, pyrazinyl, quinolinyl and quinazolinyl,

2) from 0 to about 35 weight percent of a nonionic, hydrophilic ethylenically unsaturated polymerizable monomer, and

3) from 0 to about 85 weight percent of a nonionic, hydrophobic ethylenically unsaturated polymerizable monomer in an amount sufficient to form a water-insoluble precipitate of said weakly basic polymer with all nucleic acids present in said lysate, including said target nucleic acid,

B) separating said water-insoluble precipitate from said lysate, and

C) contacting said precipitate with a base to raise the solution pH to greater than 7, and thereby releasing said nucleic acids, including said target nucleic acid, from said weakly basic polymer,

said weakly basic polymer comprising recurring units derived by addition polymerization of one or more ethylenically unsaturated polymerizable monomers having an amine group which can be protonated at acidic pH,

II) amplifying said target nucleic acid present among said released nucleic acids, and

III) detecting said amplified target nucleic acid.

8. The method of claim 7 further comprising, after step C), the step:

D) adjusting the pH of the solution containing said released nucleic acids to from about 6 to about 9.

9. The method of claim 7 wherein said amplifying is accomplished by polymerase chain reaction using a thermostable DNA polymerase and at least one labeled primer.

10. The method of claim 7 for the amplification and detection of a target nucleic acid associated with HIV1, HIV2, proviral HIV1, proviral HIV2, cytomegalovirus, Mycobacterium spp., human papilloma virus, hepatitis viruses or a genetic disease using primers specific to and hybridizable with the strands of said target nucleic acid.

11. The method of claim 8 wherein said weakly basic polymer is comprised of recurring units of from about 20 to about 100 weight percent of (a), from 0 to about 25 weight percent of (b), and from 0 to about 80 weight percent of (c).

12. The method of claim 8 wherein monomer (a) has the formula (I):

##STR3## wherein R³ is hydrogen or methyl, X is oxy or imino,

R⁴ is a divalent hydrocarbon linking group having from 1 to 8 carbon or hetero atoms in the chain and comprising one or more alkylene groups, provided that when there are more than one alkylene group, they are linked together in R⁴ with one or more carbonyl, oxy, imino, ester or amido groups in any operable combination, and R⁴ can be terminated with carbonyl, oxy, imino, ester or amido group, and

R⁵ is a cyclic amine or primary, secondary or tertiary aminoalkyl group which can be protonated at acidic pH.

13. The method of claim 12 wherein said monomer (a) has the structure (II):

##STR4## wherein R is hydrogen or methyl, and R¹ is alkylene of 1 to 3 carbon atoms.

14. The method of claim 8 wherein:

monomer (a) is selected from the group consisting of N-(3-imidazolylpropyl)methacrylamide, 1-vinylimidazole, 2-methyl-1-vinylimidazole, 2-vinylpyridine, 1-hydroxy-6-vinyl-1H-benzotriazole, 2-aminoethyl methacrylate hydrochloride, 2-aminoethyl acrylate hydrochloride, 1-vinylpyrrolidinone, 3-(N,N-dimethylamino)propyl methacrylate, 2-aminoethyl methacrylate, N-(3-aminopropyl)methacrylamide hydrochloride, 2-vinylquinoline, N-(2-imidazolylethyl)methacrylamide, N-(3-imidazolylpropyl)acrylamide, N-(imidazolylmethyl)acrylamide, N-(1,1-dimethyl-3-imidazolylpropyl)acrylamide and acid addition salts thereof,

monomer (b) is selected from the group consisting of acrylamide, 2-hydroxyethyl acrylate, 2,3-dihydroxypropyl acrylate, 2,3-dihydroxypropyl methacrylate, poly(ethyleneoxy)ethyl methacrylate (having 2 to 10 ethyleneoxy groups), and N,N-dimethyl acrylamide, and

monomer (c) is selected from the group consisting of methacrylamide, 2-hydroxyethyl methacrylate, N-t-butylmethacrylamide, ethyl acrylate, methyl methacrylate, styrene, vinyltoluene, methyl acrylate and butyl acrylate.

15. The method of claim 8 wherein said weakly basic polymer is poly[N-(3-imidazolylpropyl)methacrylamide hydrochloride-co-acrylamide], poly[N-(3-imidazolylpropyl)methacrylamide hydrochloride-co-2-hydroxyethyl methacrylate], poly(1-vinylimidazole), poly(2-aminoethyl methacrylate hydrochloride-co-2-hydroxyethyl methacrylate), poly(1-vinylimidazole-co-2-hydroxyethyl methacrylate), poly[N-(1,1-dimethyl-3-imidazolylpropyl)acrylamide] and poly(N-2-methyl-1-vinylimidazole).

16. A test kit for amplification of a target nucleic acid comprising, separately packaged:

a) an amplification reaction mixture comprising one or more amplification reagents, and

b) a weakly basic polymer comprised of recurring units derived by addition polymerization of;

1) from about 15 to 100 weight percent of a water-soluble, weakly basic ethylenically unsaturated polymerizable monomer having at least one group which can be protonated at acidic pH and which is selected from the group consisting of aminoalkyl, imidazolyl, isoxazolyl, pyridyl, piperidyl, piperazinyl, pyrazolyl, triazolyl, tetrazolyl, oxadiazolyl, pyridazinyl, pyrimidyl, pyrazinyl, quinolinyl and quinazolinyl,

2) from 0 to about 35 weight percent of a nonionic, hydrophilic ethylenically unsaturated polymerizable monomer, and

3) from 0 to about 85 weight percent of a nonionic, hydrophobic ethylenically unsaturated polymerizable monomer.

17. The test kit of claim 16 wherein said amplification reaction mixture comprises a set of primers, at least one of which is labeled, a plurality of dNTP'"'"'s and a thermostable DNA polymerase.

18. The test kit of claim 16 comprising a test device containing one or more kit components.

19. The test kit of claim 16 wherein said weakly basic polymer is attached to a solid substrate.

20. A method for the amplification and detection of a target nucleic acid comprising:

I) lysing cells or virus particles to release a target nucleic acid,

II) subjecting said target nucleic acid to the steps of;

A) at a pH of less than 7, contacting said target nucleic acid with a water-soluble, weakly basic polymer comprised of recurring units derived by addition polymerization of;

1) from about 15 to 100 weight percent of a water-soluble, weakly basic ethylenically unsaturated polymerizable monomer having at least one group which can be protonated at acidic pH and which is selected from the group consisting of aminoalkyl, imidazolyl, isoxazolyl, pyridyl, piperidyl, piperazinyl, pyrazolyl, triazolyl, tetrazolyl, oxadiazolyl, pyridazinyl, pyrimidyl, pyrazinyl, quinolinyl and quinazolinyl,

2) from 0 to about 35 weight percent of a nonionic, hydrophilic ethylenically unsaturated polymerizable monomer, and

3) from 0 to about 85 weight percent of a nonionic, hydrophobic ethylenically unsaturated polymerizable monomer in an amount sufficient to form a water-insoluble precipitate of said weakly basic polymer with all nucleic acids present in said lysate, including said target nucleic acid,

B) separating said water-insoluble precipitate from said lysate, and

C) contacting said precipitate with a base to raise the solution pH to greater than 7, and thereby releasing said nucleic acids, including said target nucleic acid, from said weakly basic polymer,

said weakly basic polymer comprising recurring units derived by addition polymerization of one or more ethylenically unsaturated polymerizable monomers having an amine group which can be protonated at acidic pH,

III) without further adjustment of pH, amplifying said released target nucleic acid, and

IV) detecting said amplified target nucleic acid.

21. The method of claim 20 wherein said weakly basic polymer is water-insoluble at basic pH, and said method further comprises the step of removing said water-insoluble polymer after release of said target nucleic acid therefrom and prior to amplification thereof.