DETECTION OF METHYLATED DNA AND DNA MUTATIONS

• US 20100292348A1
• Filed: 10/01/2008
• Published: 11/18/2010
• Est. Priority Date: 10/01/2007
• Status: Active Grant

• Current Assignee: University of Southern California
• Original Assignee: University of Southern California
• Inventors: Cote, Richard James, Yang, Allen S., Thompson, Mark E., Zhou, Chongwu
• Granted Patent: US 8,609,333 B2
• Time in Patent Office: Days
• US Class Current: 514/789
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2522/10 Nucleic acid binding proteins
• CPC Class Codes: C12Q 2522/101 Single or double stranded nucleic acid binding proteins
• CPC Class Codes: C12Q 2523/125 Bisulfite(s)
• CPC Class Codes: C12Q 2537/164 Methylation detection other then bisulfite or methylation sensitive restriction endonucleases
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 27/4146 involving nanosized elements, e.g. nanotubes, nanowires
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention relates to various methods of detecting DNA methylation and defected DNA. In one embodiment, the invention provides a nanosensor bound to a probe that is complementary to a DNA methylation sequence.

Claims

1. A method of preparing a nanosensor to detect DNA methylation, comprising:

providing a nanosensor; and

attaching a probe to the nanosensor,

wherein the probe is adapted to bind a methylated DNA sequence.

2. The method of claim 1, wherein the nanosensor comprises nanotube and nanowire surfaces.

3. The method of claim 1, wherein the nanosensor is an NW/NT sensor.

4. The method of claim 1, wherein the probe comprises a polynucleotide.

5. The method of claim 1, wherein the probe is adapted to bind an agent.

6. The method of claim 5, wherein the agent comprises a signal amplifier.

7. The method of claim 1, wherein the probe comprises SEQ. ID. NO.:

1, SEQ. ID. NO.;

2, SEQ. ID. NO.;

3, SEQ. ID. NO.;

4, or a combination thereof.

8. The method of claim 1, wherein the probe comprises SEQ. ID. NO.:

5, SEQ. ID. NO.;

6, SEQ. ID. NO.;

7, SEQ. ID. NO.;

8, SEQ. ID. NO.;

9, SEQ. ID. NO.;

10, SEQ. ID. NO.;

11, SEQ. ID. NO.;

12, SEQ. ID. NO.;

13, or a combination thereof.

9. A nanosensor for detecting defected DNA, comprising:

a NW/NT sensor; and

a probe bound thereto,

wherein the probe is adapted to bind to a defected DNA.

10. The nanosensor of claim 9, wherein the probe is a polynucleotide.

11. The nanosensor of claim 10, wherein the polynucleotide comprises a CG rich sequence.

12. The nanosensor of claim 9, wherein the defected DNA comprises a methylated nucleotide.

13. The nanosensor of claim 9, wherein the defected DNA comprises a point mutation.

14. The nanosensor of claim 9, wherein the probe and defected DNA are adapted to bind as complementary polynucleotides.

15. A method of detecting a defected nucleotide in a DNA sample, comprising:

providing a nanosensor configured to detectably change when a defected nucleotide bound to a probe on the nanosensor is itself bound by an agent;

contacting the nanosensor with a sample; and

contacting the nanosensor with the agent,

wherein the nanosensor detectably changes if the sample comprises the defected nucleotide.

16. The method of claim 15, wherein the agent comprises a methyl-CpG binding protein.

17. The method of claim 15, wherein the agent comprises MBD1, MBD2, MBD4 and/or MeCP272.

18. The method of claim 15, wherein the agent comprises an antibody.

19. The method of claim 15, wherein the defected nucleotide comprises a point mutation.

20. The method of claim 15, wherein the agent comprises a DNA repair protein.

21. The method of claim 15, wherein the defected nucleotide comprises a methylated DNA nucleotide.

22. A method of diagnosing a disease in an individual in which the presence or absence of methylation for a plurality of genetic loci is associated with the disease, comprising:

using a nanosensor to determine the presence or absence in the individual of the methylation in the plurality of genetic loci; and

diagnosing the individual as having the disease if the individual demonstrates the presence or absence of the methylation of the plurality of genetic loci.

23. The method of claim 22, wherein the disease is cancer.

24. A method of treating a disease in an individual in which the presence or absence of methylation for a plurality of genetic loci is associated with the disease, comprising:

using a nanosensor to determine the presence or absence in the individual of the methylation in the plurality of genetic loci;

diagnosing the individual as having the disease if the individual demonstrates the presence or absence of the methylation of the plurality of genetic loci; and

treating the disease, if the individual is diagnosed as having it.

25. The method of claim 24, wherein the disease is cancer.