Method for Sensitive Detection of Target DNA Using Target-Specific Nuclease

• US 20170191123A1
• Filed: 05/28/2015
• Published: 07/06/2017
• Est. Priority Date: 05/28/2014
• Status: Abandoned Application

• Current Assignee: Institute for Basic Science, Toolgen Incorporated
• Original Assignee: Institute for Basic Science, Toolgen Incorporated
• Inventors: Lee, Seung Hwan, Kim, Jin Soo, Kim, So Jung, Kim, Seok Joong
• Application Number:
  US15/314,288
• Publication Number:
  US 20170191123A1
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6848 characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2537/162 Helper probe
• CPC Class Codes: G01N 2800/245 Transplantation related diseases, e.g. graft versus host disease
• CPC Class Codes: G01N 2800/52 Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
• CPC Class Codes: G01N 33/53 Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/574 for cancer

Abstract

The present invention relates to a method for analyzing a genotype using a target-specific nuclease and, specifically, to a method for diagnosing cancer or analyzing a genotype by removing wild type DNA or particular genotype DNA using a target-specific nuclease or a variant thereof to amplify or concentrate only a small amount of DNA which has a difference in variation, such as a mutation, or genotype, and to a method for separating target DNA sesusing a target-specific nuclease or a variant thereof. Such methods are novel paradigm methods contrary to existing simple target-specific nucleases for post-PCR recognition of normal genotype and carcinogenic genotype, and can be favorably used in the early diagnosis of cancer or analysis of similar genotypes.

Claims

1. A method for analyzing a genotype comprising:

(i) removing particular genotype DNA in an isolated sample, in which two or more genotypes of DNA are mixed, by cleaving the particular genotype DNA using a nuclease specific to the particular genotype DNA; and

(ii) analyzing other genotype DNA present in the isolated sample, in which the particular genotype DNA has been removed.

2. The method of claim 1, comprising:

(a) removing the particular genotype DNA in the isolated sample, in which two or more genotypes of DNA are mixed, by cleaving the particular genotype DNA, using the nuclease specific to the particular genotype DNA;

(b) amplifying other genotype DNA present in the isolated sample, in which the particular genotype DNA has been removed; and

(c) analyzing the amplified other genotype DNA.

3. The method of claim 1, wherein the nuclease is selected from the group consisting of a zinc finger nuclease (ZFN), a transcription activator-like effector nuclease (TALEN), and an RNA-guided engineered nuclease (RGEN).

4. The method according to claim 1, which is for diagnosis of cancer, wherein:

step (i), in which the particular genotype DNA is wild type DNA, is to remove the wild type DNA by cleaving the wild type DNA using the nuclease specific to the wild type DNA in the isolated sample; and

step (ii), in which other genotype DNA is DNA having a cancer-specific mutation, is to analyze the cancer-specific mutant DNA in the isolated sample, in which the wild type DNA is removed.

5. The method of claim 4, wherein the diagnosis of cancer is an early diagnosis of cancer.

6. The method of claim 4, wherein the diagnosis of cancer is predicting the prognosis of cancer.

7. The method of claim 4, wherein the isolated sample, in which two or more genotypes of DNA are mixed, is a blood sample isolated from a subject suspected of having cancer.

8. The method of claim 1, which is for predicting the prognosis of a subject that has received cell or organ transplantation, wherein:

step (i), in which the particular genotype DNA is the DNA of a subject that has received cell or organ transplantation, is to remove the DNA of the subject in a sample, which is isolated from the subject that has received cell or organ transplantation and comprises two or more genotypes of DNA, by cleaving the DNA of the subject using a nuclease specific to the DNA of the subject; and

step (ii), in which other genotype DNA is the DNA of a transplanted cell or organ, comprises analyzing the DNA of the transplanted cell or organ in the sample in which the DNA of the subject has been removed.

9. The method for claim 1, which is collecting information regarding a crime scene, wherein:

step (i), in which the particular genotype DNA is the DNA of a victim, is to remove the DNA of the victim in an isolated DNA sample, which is derived from the crime scene and comprises two or more genotypes of DNA, by cleaving the DNA of the victim using a nuclease specific to the DNA of the victim; and

step (ii), in which other genotype DNA is the DNA of an assailant, comprises analyzing the DNA of the assailant in the sample in which the DNA of the victim has been removed.

10. The method of claim 1, which is for collecting information regarding a crime scene, wherein:

step (i), in which the particular genotype DNA is the DNA of an assailant, is to remove the DNA of the assailant in an isolated DNA sample, which is derived from the crime scene and comprises two or more genotypes of DNA, by cleaving the DNA of the assailant using a nuclease specific to the DNA of the assailant; and

step (ii), in which other genotype DNA is the DNA of a victim, comprises analyzing the DNA of the victim in the sample in which the DNA of the assailant has been removed.

11. A method for analyzing a genotype comprising:

(i) removing other genotype DNA by cleaving the other genotype DNA while masking particular genotype DNA in an isolated sample, in which two or more genotypes of DNA are mixed, for protection from cleavage by RGEN capable of recognizing the other genotype DNA, using a guide RNA (gRNA) specific to the particular genotype DNA and an inactivated Cas nuclease protein (dCas); and

(ii) analyzing the particular genotype DNA present in the sample, in which the other genotype DNA has been removed.

12. The method of claim 11, comprising:

(a) removing other genotype DNA by cleaving the other genotype DNA while masking the particular genotype DNA in an isolated sample, in which two or more genotypes of DNA are mixed, for protection from cleavage by RGEN capable of recognizing the other genotype DNA, using a guide RNA (gRNA) specific to the particular genotype DNA and an inactivated Cas nuclease protein (dCas);

(b) amplifying the particular genotype DNA in a sample, in which the other genotype DNA has been removed; and

(c) analyzing the amplified particular genotype DNA.

13. The method of claim 11, which is for diagnosing cancer, wherein:

step (i), in which other genotype DNA is wild type DNA, and particular DNA is DNA having a cancer-specific mutation, is to remove the wild type DNA in an isolated sample by cleaving the wild type DNA while masking the particular genotype DNA for protection from cleavage by RGEN specific to the wild type DNA, using a guide RNA capable of specifically binding to the particular DNA having the cancer-specific mutation and an inactivated Cas nuclease protein (dCas); and

step (ii) is to analyze the DNA having the cancer-specific mutation present in the isolated sample, in which the wild type DNA has been removed.

14. The method of claim 13, wherein the diagnosing cancer is an early diagnosis of cancer.

15. The method of claim 13, wherein the diagnosing cancer is predicting the prognosis of cancer.

16. The method of claim 13, wherein the isolated sample, in which two or more genotypes of DNA are mixed, is a blood sample isolated from a subject suspected of having cancer.

17. The method of claim 11, which is for predicting the prognosis of a subject that has received cell or organ transplantation, wherein:

step (i), in which other genotype DNA is the DNA of a subject that has received cell or organ transplantation, and the particular genotype DNA is the DNA of a transplanted cell or organ, is to remove the DNA of the subject that has received cell or organ transplantation in an isolated sample by cleaving the DNA of the subject that has received cell or organ transplantation while masking the particular genotype DNA for protection from cleavage by RGEN specific to the DNA of the subject that has received cell or organ transplantation, using a guide RNA capable of specifically binding to the DNA of the transplanted cell or organ and an inactivated Cas nuclease protein (dCas); and

step (ii) is to analyze the DNA of the transplanted cell or organ present in the sample in which the DNA of the subject that has received the cell or organ transplantation has been removed.

18. The method of claim 11, which is for collecting information regarding a crime scene, wherein:

step (i), in which other genotype DNA is the DNA of a victim, and the particular genotype DNA is the DNA of an assailant, is to remove the DNA of the victim in an isolated sample by cleaving the DNA of the victim while masking the particular genotype DNA for protection from cleavage by RGEN specific to the DNA of the victim, using a guide RNA capable of specifically binding to the DNA of the assailant and an inactivated Cas nuclease protein (dCas); and

step (ii) is to analyze the DNA of the assailant present in the sample in which the DNA of the victim has been removed.

19. The method of claim 11, which is for collecting information regarding a crime scene, wherein:

step (i), in which other genotype DNA is the DNA of an assailant, and the particular genotype DNA is the DNA of a victim, is to remove the DNA of the assailant in an isolated sample by cleaving the DNA of the assailant while masking the particular genotype DNA for protection from cleavage by RGEN specific to the DNA of the assailant, using a guide RNA capable of specifically binding to the DNA of the victim and an inactivated Cas nuclease protein (dCas); and

step (ii) is to analyze the DNA of the victim present in the sample, in which the DNA of the assailant has been removed.

20. The method of claim 11, wherein the inactivated Cas protein lacks DNA cleavage activity of Cas proteins.

21. The method of claim 20, wherein the inactivated Cas protein is a variant of a Cas9 protein having a D10A, H840A, or D10A/H840A mutation.

22. A method for analyzing a genotype of DNA in an isolated sample comprising:

(i) removing DNA of a non-pathogenic bacterium or virus in the isolated sample by cleaving the DNA of the non-pathogenic bacterium or virus by treating the DNA of the non-pathogenic bacterium or virus with a nuclease specific to the DNA of the non-pathogenic bacterium or virus, in the isolated sample having DNA of bacteria or viruses; and

(ii) analyzing DNA of a pathogenic bacterium or virus in the isolated sample in which the DNA of the non-pathogenic bacterium or virus has been removed.

23. The method of claim 22, comprising:

(a) removing the DNA of the non-pathogenic bacterium or virus by cleaving the DNA of the non-pathogenic bacterium or virus by treating the DNA of the non-pathogenic bacterium or virus with a nuclease specific to the DNA of the non-pathogenic bacterium or virus, in the isolated sample having the DNA of bacteria or viruses;

(b) amplifying the DNA of a pathogenic bacterium or virus in the isolated sample in which the DNA of the non-pathogenic bacterium or virus has been removed; and

(c) analyzing the amplified DNA of the pathogenic bacterium or virus.

24. The method of claim 22, wherein the nuclease is selected from the group consisting of a zinc finger nuclease (ZFN), a transcription activator-like effector nuclease (TALEN), and an RNA-guided engineered nuclease (RGEN).

25. A method for analyzing a genotype of DNA in an isolated sample comprising:

(i) removing DNA of a non-pathogenic bacterium or virus in the isolated sample by cleaving the DNA of the non-pathogenic bacterium or virus while masking DNA of a pathogenic bacterium or virus for protection from cleavage by RGEN specific to the non-pathogenic bacterium or virus, using a guide RNA specific to the pathogenic bacterium or virus and an inactivated Cas nuclease protein (dCas); and

(ii) analyzing the DNA of the pathogenic bacterium or virus in the isolated sample in which the DNA of the non-pathogenic bacterium or virus has been removed.

26. The method of claim 25, comprising:

(a) removing the DNA of the non-pathogenic bacterium or virus in the isolated sample by cleaving the DNA of the non-pathogenic bacterium or virus while masking the DNA of a pathogenic bacterium or virus for protection from cleavage by RGEN specific to the non-pathogenic bacterium or virus, using a guide RNA specific to the DNA of the pathogenic bacterium or virus and an inactivated Cas nuclease protein (dCas);

(b) amplifying the DNA of the pathogenic bacterium or virus in the isolated sample in which the DNA of the non-pathogenic bacterium or virus has been removed; and

(c) analyzing the amplified DNA of the pathogenic bacterium or virus.