Novel dna chips

• US 20030186262A1
• Filed: 12/03/2002
• Published: 10/02/2003
• Est. Priority Date: 03/01/2000
• Status: Abandoned Application

• Current Assignee: Nucleica
• Original Assignee: Nucleica
• Inventors: Cailloux, Fabrice
• Application Number:
  US10/220,507
• Publication Number:
  US 20030186262A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/125 incorporating agents resulting in resistance to degradation
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode

Abstract

The invention concerns a DNA chip system for detecting mutation in a target nucleic acid such that only the DNA comprising the mutation remains on the chip at the end of the process. The invention concerns a method which consists in adding a complementary αS-phosphothioatedesoxynucleotide of the mutation is added by means of DNA polymorase at the 3′ end of the probe hybridised with the target nucleic acid and in adding an exonuclease so that only the elongated probes are not degraded. The detection of the presence or absence of mutation is carried out by directly or indirectly measuring the presence or the absence of DNA in a specific site on the chip. Advantageously, the chip comprises ISFET transistors or piezoelectric transducers.

Claims

1. A method for detecting a mutation at position n in a target nucleic acid, characterized in that it comprises the following steps:

a) hybridization of a probe linked in 5′

to a solid support of the DNA chip type with a target nucleic acid, the 3′

end of said probe hybridizing at most up to nucleotide n-1 of the target nucleic acid;

b) elongation of the probe hybridized in step a) by incorporation, in the 5′

-3′

direction of nucleotides complementary to said target nucleic acid by means of a reaction mixture comprising at least one nucleotide derivative resistant to degradation by an exonuclease and a DNA polymerase,

c) digestion with said exonuclease such that only the probes elongated in step b) are not degraded, washing,

d) detection of the presence or absence of mutation by directly or indirectly measuring the presence or absence of DNA.

2. The method as claimed in claim 1, characterized in that the presence or absence of mutation is detected in step d) by measuring the modification of a property of the solid support linked to the presence or absence of DNA.

3. The method as claimed in claim 1, characterized in that the presence or absence of mutation is detected in step d) by optical reading of the presence or absence of DNA.

4. The method as claimed in claim 2, characterized in that there is measured in step d) a variation of a physicochemical, electrical, optical or mechanical characteristic of the solid support in particular chosen from charge, doping, conductivity, resistance, impedance or any other effect of electrical variation, of the field effect or alternatively any variation of mass causing a variation of field, of the frequency of resonance or of electroacoustic admittance, of the refractive index of the support, in particular ellipsometry, of the evanescent waves comprising the measurement of SPR (surface plasmon resonance), of Brewster'"'"'s angle of refraction, of the critical angle of reflection, FTR (frustrated total reflection), or STIR (scattered total internal reflection).

5. The method as claimed in claim 2, characterized in that the solid support consists of a DNA chip comprising a material selected from semi-conductors, dielectrics and piezoelectric transducers or a gold-prism structure.

6. The method as claimed in claim 5, characterized in that the solid support comprises structures of the Metal-Oxide-Semiconductor (MOS), preferably Electrolyte-Oxide-Semiconductor (EOS), type.

7. The method as claimed in claim 5, characterized in that the solid support comprises field effect transistors (FET), in particular ISFET or ENFET type transistors.

8. The method as claimed in claim 5, characterized in that a group containing a metal atom is grafted onto the probes, in particular a ferrocene group.

9. The method as claimed in claim 3, characterized in that step d) consists in measuring the quantity of light transmitted through the solid support, said support being made of a transparent material, in particular glass.

10. The method as claimed in claim 3, characterized in that step d) consists in measuring the fluorescence of the probes labeled beforehand.

11. The method as claimed in either of claims 9 and 10, characterized in that the optical reading is carried out by a CCD camera.

12. The method as claimed in one of claims 1 to 11, characterized in that there is used in step b) an α

S-phosphothioatedexoynucleotide, preferably α

S-dATP, α

S-dTTP, α

S-dCTP, α

S-dGTP, α

S-dUTP or α

S-dITP.

13. The method as claimed in one of claims 1 to 12, characterized in that exonuclease III is used in step c).

14. The method as claimed in claims 1 to 13, characterized in that step b) is carried out in parallel on 4 sites for each probe, with addition of a reaction mixture comprising a different α

S-phosphothioatedexoynucleotide per site.

15. The method as claimed in one of the preceding claims, intended for the detection of mutations of genes involved in diseases, in particular in inherited genetic diseases, in particular hemochromatosis, sickle cell anemia, β

and α

thalassemias, cystic fibrosis, hemophilia, and mutations in the genes involved in cancer.

16. The method as claimed in one of the preceding claims, intended for studying the polymorphism of genes or of any genetic region.

17. The method as claimed in one of the preceding claims, intended for the detection and/or identification of genetically modified organisms (GMO).

18. A device which makes it possible to carry out the method as claimed in one of the preceding claims.

19. A device as claimed in claim 18, characterized in that it comprises a system for detecting the presence or absence of DNA at a specific site of a chip, in particular a piezoelectric transducer, a field effect transducer, an optical density or fluorescence reader.

20. A kit comprising a DNA chip to which there are attached probes and at least one of the elements chosen from:

a batch of 4 reaction mixtures each comprising a different α

S-phosphothioatedexoynucleotide selected from α

S-dATP, α

S-dTTP, α

S-dCTP and α

S-dGTP, α

S-dUTP and α

S-dITP,

a DNA polymerase,

an exonuclease, in particular exonuclease III,

a batch of solutions for solubilizing the DNA polymerase and/or the exonuclease in the case where these enzymes exist in the form of a powder.

21. The kit as claimed in claim 20, characterized in that the chips comprise a solid support of the ISFET or ENFET type.

22. The kit as claimed in either of claims 20 and 21, characterized in that it is intended for the detection of mutations of genes involved in diseases, in particular in inherited genetic diseases and in cancer.

23. The kit as claimed in either of claims 20 and 21, characterized in that it is intended for the detection of SNPs (Single Nucleotide Polymorphism).

24. The kit as claimed in either of claims 20 and 21, characterized in that it is intended for the detection and/or identification of genetically modified organisms (GMO).