Method of detecting nucleic acid sequences

• US 4,808,519 A
• Filed: 11/22/1985
• Issued: 02/28/1989
• Est. Priority Date: 04/06/1984
• Status: Expired due to Term

• Current Assignee: Life Technologies Incorporated (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Incorporated (Thermo Fisher Scientific Incorporated)
• Inventors: Hartley, James L., Berninger, Mark S.
• Primary Examiner(s): Warren, Charles F.
• Assistant Examiner(s): NOT, DEFINED
• Application Number:
  US06/804,647
• Time in Patent Office: 1,194 Days
• Field of Search: 435/6, 435/27, 435/29, 435/91, 435/172.3, 435/253, 435/317, 435/320, 435/803, 436/501, 536/27, 935/78
• US Class Current: 435/6.16
• CPC Class Codes: C12N 15/64 General methods for preparing the vector, for introducing it into the cell or for selecting the vector-containing host
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/706 for hepatitis
• CPC Class Codes: Y10S 435/803 Physical recovery methods, e.g. chromatography, grinding

Abstract

A process for detecting specific nucleotide sequences, called targets, in which a special DNA probe molecule, called a probe-vector, is capable of transforming bacteria if and only if it is held in a circular configuration by base pairing to a target nucleic acid, said transformation resulting in the detection of a phenotype specified by the probe-vector, said detection establishing the presence, absence, or quantity of the target; and a probe-vector molecule for performing the process.

Claims

1. A probe-vector molecule used for detecting a target nucleic acid containing a particular base sequence X₁ X₂ X₃ . . . X_m . . . Y₁ Y₂ Y₃ . . . Y_n, said probe-vector comprising

a linear partially single stranded DNA molecule comprised of two strands, a long strand containing the sequence X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ . . . Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'hd p . . . Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁, and a short strand containing the sequence Z₁ Z₂ Z₃ . . . Z_p, wherein m, n, p and k are integers, and in which

for any k, X'"'"'_k is the base complementary to X_k is the base complementary to Y_k, and Z'"'"'_k is the base complementary to Z_K, the ends of said long strand of said probe-vector being substantially complementary to sections of said target nucleic acid,

m and n are sufficiently large so that when said probe-vector is added to said target nucleic acid under hybridizing conditions, stable hybridization will occur between the ends of said long strand of said probe-vector and the said substantially complementary section of said target nucleic acid forming thereby a circular hybrid, the probe-vector being circularized if the particular target sequence is present and has hybridized to said probe-vector, and

the regions Z₁ Z₂ Z₃ . . . Z_p and Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'_p of said probe-vector strands contain a replicon and confer a detectable phenotype such that bacteria transformed by said hybrid are detectable and distinguishable from untransformed bacteria by detection of said phenotype.

2. The probe-vector molecule of claim 1 in which the segments X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ of the probe-vector are substantially complementary to target regions X₁ X₂ X₃ . . . X_m-1 X_m and Y₁ Y₂ Y₃ . . . Y'"'"'_n-1 Y'"'"'_n, said target regions being non-contiguous and separated by a segment W₁ W₂ W₃ . . . W_q, where q is an integer

such that in the circular hybrid the ends of the long strand of said probe-vector are separated from each other by not hyridizing with the target nuclei acid segment W₁ W₂ W₃ . . . W_q.

3. A method for determining the presence, in a mixture of DNA, of a target nucleic acid containing a particular base sequence X₁ X₂ X₃ . . . X_m . . . Y₁ Y₂ Y₃. . . Y_n, said method requiring the use of a probe-vector having a long strand and a short strand or just a long strand, wherein the long strand comprises the sequence X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ . . . Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'_p . . . Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁, and the short strand comprises the sequence Z₁ Z₂ Z₃ . . . Z_p, where m, n, p and k are integers and wherein

for any k, X'"'"'_k is the base complementary to X_k, Y'"'"'_k is the base complementary to Y_k, and Z'"'"'_k is the base complementary to Z_k, the ends of said long strand of said probe-vector being substantially complementary to sections of said target nucleic acid,

m and n are sufficiently large so that when said probe-vector is added to said target nucleic acid under hybridizing conditions, stable hybridization will occur between the ends of said long strand of said probe-vector and the said substantially complementary section of said target DNA forming thereby a circular hybrid, the probe-vector being circularized if the particular target sequence is present and has hybridized to said prove-vector, and

the regions Z₁ Z₂ Z₃ . . . Z_p and Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'_p of said probe vector strands contain a replicon and confer a detectable phenotype such that bacteria transformed by said hybrid are detectable and distinguishable from untransformed bacteria by detection of said phenotype,

said method comprising the following steps:

(A) introducing said probe-vector to the sample containing nucleic acids, said nucleic acids being single stranded or being made single stranded before or after the addition of probe-vector, said mixture of sample and probe-vector comprising the test mixture;

(B) adjusting the conditions of the test mixture to hybridization conditions, such conditions being favorable for the formation of circular hybrids between said long strand and short strand or only with said long strand together with said target if said target is present in the sample, but such conditions being unfavorable for the formation of hybrids between non-target nucleic acids and probe-vector, the test mixture after hybridization comprising the hybridization mixture;

(C) introducing said hybridization mixture to bacterial cells, said bacterial cells being predisposed to transformation by circular DNA molecules but not by linear DNA molecules, said introduction being made under conditions which allow transformation by said circular hybrid but not by linear probe-vector, said bacterial cells lacking the detectable phenotype conferred by said probe-vector, said mixture of bacterial cells and hybridization mixture comprising the transformation mixture;

(D) adjusting the conditions of the transformation mixture to allow detection of the phenotypic marker, said phenotypic marker being exhibited only by transformed cells, such a mixture comprising the detection mixture; and

(E) detecting the phenotypic marker in the detection mixture.

4. The method of claim 3 in which the X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ segments are substantially complementary to target regions X_m X_m-1 . . . X₃ X₂ X₁ and Y_n Y_n-1 . . . Y₃ Y₂ Y₁, said target regions being non contiguous and separated by a segment W₁ W₂ W₃ . . . W_q, said method resulting in the detection of the target and also resulting in the cloning of the region W₁ W₂ W₃ . . . W_q of the target, said region lacking a complementary region on the probe-vector, wherein q is an integer.

5. The method of claim 3 in which the bacteria are Escherichia coli and the region Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'_p of the probe-vector contains a replicon which functions in E. coli and a phenotypic marker which is detectable in E. coli.

6. The method of claim 4 in which the bacteria are Escherichia coli and the region Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'_p of the probe-vector contains a replicon which functions in E. coli and a phenotypic marker which is detectable in E. coli.

7. The method of claim 3 in which the region Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'_p of the probe-vector contains the replicon of the plasmid pBR322 and the ampicillin resistance gene of the plasmid pBR322.

8. The method of claim 4 in which the region Z'"'"'₁ Z'"'"'₂ Z'"'"'₃ . . . Z'"'"'_p of the probe-vector contains the replicon of the plasmid pBR322 and the ampicillin resistance gene of the plasmid pBR322.

9. The method of claim 3 in which the conditions of the detection mixture are adjusted by placing the detection mixture on solid agar plates formulated to allow the growth of bacterial cells which have been transformed by the circular hybrid, but which will allow the growth of bacterial cells which have not been transformed by said hybrid, incubating said agar plates under appropriate conditions to effect selection of transformed bacterial cells and determining the number of bacterial colonies on the plates, this number constituting a measure of the amount of target nucleic acid present in the same.

10. The method of claim 4 in which the conditions of the detection mixture are adjusted by placing the detection mixture on solid agar plates formulated to allow the growth of bacterial cells which have been transformed by the circular hybrid, but will not allow the growth of bacterial cells which have not been transformed by said hybrid, incubating said agar plates under appropriate conditions to effect selection of transformed bacterial cells and determining the number of bacterial colonies on the plates, this number constituting a measure of the amount of target nucleic acid present in the sample.

11. The method of claim 7 in which the conditions of the detection mixture are adjusted by placing the detection mixture on solid agar plates formulated to allow the growth of bacterial cells which have been transformed by the circular hybrid, but which will not allow the growth of bacterial cells which have not been transformed by said hybrid, incubating said agar plates under appropriate conditions to effect selection of transformed bacterial cells and determining the number of bacterial colonies on the plates, this number constituting a measure of the amount of target nucleic acid present in the sample.

12. The method of claim 3 in which the conditions of the detection mixture are adjusted by placing the detection mixture on solid agar plates containing the antibiotic ampicillin present in an amount sufficient to allow the growth of bacterial cells which have been transformed by the circular hybrid, but which prevents growth of bacterial cells which have not been transformed by said hybrid, said hybrid containing a gene conferring resistance to ampicillin on bacterial cells harboring the hybrid;

incubating said agar plates at a suitable temperature to effect selection of transformed bacterial cells and determining the number of ampicillin resistant colonies, said number constituting a measure of the amount of target nuclei acid present in the sample.

13. The method of claim 4 in which the conditions of the detection mixture are adjusted by placing the detection mixture on solid agar plates containing the antibiotic ampicillin present in an amount sufficient to allow the growth of bacterial cells which have been transformed by the circular hybrid, but which prevents growth of bacterial cells which have not been transformed by said circular hybrid, said hybrid containing a gene conferring resistance to ampicillin on bacterial cells harboring the hybrid;

incubating said agar plates at a suitable temperature to effect selection of transformed bacterial cells and determining the number of ampicillin resistant colonies, said number constituting a measure of the amount of target nucleic acid present in the sample.

14. The method of claim 7 in which the conditions of the detection mixture are adjusted by placing the detection mixture on solid agar plates containing the antibiotic ampicillin present in an amount sufficient to allow the growth of bacterial cells which have been transformed by the circular hybrid, but which prevents growth of bacterial cells which have not been transformed by said hybrid, said hybrid containing a gene conferring resistance to ampicillin on bacterial cells harboring the hybrid;

incubating said agar plates at a suitable temperature to effect selection of transformed bacterial cells and determining the number of ampicillin resistant colonies, said number constituting a measure of the amount of target nucleic acid present in the sample.

15. The method of claim 9 in which the conditions of the detection mixture are adjusted by placing the detection mixture on solid agar plates containing the antibiotic ampicillin present in an amount sufficient to allow the growth of bacterial cells which have been transformed by the circular hybrid, but which prevents growth of bacterial cells which have not been transformed by said hybrid, said hybrid containing a gene conferring resistance to ampicillin on bacterial cells harboring the hybrid;

incubating said agar plates at a suitable temperature to effect selection of transformed bacterial cells and determining the number of ampicillin resistant colonies, said number constituting a measure of the amount of target nucleic acid present in the sample.

16. The method of claim 3 in which the target is viral DNA and in which the regions X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ of the probe-vector are complementary to a region of the viral DNA.

17. The method of claim 3 in which the target is X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ which are complementary to a region of the hepatitis B viral DNA or to the entire hepatitis B viral DNA.

18. The method of claim 3 in which the target is viral DNA and in which the regions X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ of the probe-vector are complementary to a region of the viral DNA.

19. The method of claim 4 in which the target is viral DNA and in which the regions X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ of the probe-vector are complementary to a region of the viral DNA.

20. The method of claim 3 in which the target is hepatitis B DNA and the probe-vector contains regions X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ which are complementary to a region of the hepatitis B viral DNA or to the entire hepatitis B viral DNA.

21. The method of claim 4 in which the target is hepatitis B DNA and prove-vector contains regions X'"'"'_m X'"'"'_M-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_N-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ which are complementary to a region of the hepatitis B viral DNA or to the entire hepatitis B viral DNA.

22. The method of claim 5 in which the target is viral DNA and in which the regions X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ of the probe-vector are complementary to a region of the viral DNA.

23. The method of claim 7 in which the target is viral DNA and in which the regions X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ of the probe-vector are complementary to a region of the viral DNA.

24. The method of claim 18 in which the target is X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y_n Y_n-1 . . . Y₃ Y₂ Y₁ which are complementary to a region of the hepatitis B viral DNA or to the entire hepatitis B viral DNA.

25. The method of claim 5 in which the target is hepatitis B DNA anb probe-vector contains regions X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ which are complementary to a region of the hepatitis B viral DNA or to the entire hepatitis B viral DNA.

26. The method of claim 7 in which the target is X'"'"'_m X'"'"'_M-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ which are complementary to a region of the hepatitis B viral DNA or to the entire hepatitis B viral DNA.

27. The method of claim 12 in which the target is X'"'"'_m X'"'"'_m-1 . . . X'"'"'₃ X'"'"'₂ X'"'"'₁ and Y'"'"'_n Y'"'"'_n-1 . . . Y'"'"'₃ Y'"'"'₂ Y'"'"'₁ which are complementary to a region of the hepatitis B viral DNA or to the entire hepatitis B viral DNA.