Sensor arrays and nucleic acid sequencing applications

• US 20060199193A1
• Filed: 09/13/2005
• Published: 09/07/2006
• Est. Priority Date: 03/04/2005
• Status: Active Grant

• Current Assignee: Intel Corporation
• Original Assignee: Intel Corporation
• Inventors: Dubin, Val M., Yamakawa, Mineo, Su, Xing, Koo, Tae-Woong, Chan, Selena, Jingwu, Zhang
• Granted Patent: US 9,040,237 B2
• Time in Patent Office: Days
• US Class Current: 435/6.16
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 27/414 Ion-sensitive or chemical field-effect transistors, i.e. ISFETS or CHEMFETS
• CPC Class Codes: G01N 27/4145 specially adapted for biomolecules, e.g. gate electrode with immobilised receptors
• CPC Class Codes: G01N 27/4148 Integrated circuits therefor, e.g. fabricated by CMOS processing CMOS processing per se H01L21/82

Abstract

Embodiments of the present invention provide devices methods for sequencing DNA using arrays of reaction cavities containing sensors to monitor changes in solutions contained in the reaction cavities. Additional embodiments provide devices and methods for sequencing DNA using arrays of reaction cavities that allow for optical monitoring of solutions in the reaction cavities. Test and fill reaction schemes are disclosed that allow DNA to be sequenced. By sequencing DNA using parallel reactions contained in large arrays, DNA can be rapidly sequenced.

Claims

1. ) A method for determining the sequence of a sample of DNA to be sequenced comprising,

providing an array comprised of a plurality of cavities to hold reactants, the cavities having a surface for attachment of DNA and a coupled sensor for detecting changes in a solution;

attaching DNA to the surfaces of the cavities so that statistically one DNA molecule is attached in one cavity;

terminating a primer strand of DNA hybridized to the DNA to be sequenced with a nuclease-resistant nucleotide;

providing reactants to the cavities comprising a nucleotide base, an enzyme capable of extending a DNA molecule, and an enzyme capable of deconstructing a DNA molecule under conditions that allow DNA to be synthesized and deconstructed;

monitoring the cavities to detect changes in the reactants in the cavities;

repeating the elements of terminating the primer strand of DNA, providing reactants to the cavities, and monitoring the cavities at least one time; and

determining sequence information for the sample of DNA to be sequenced based on changes detected in the reactants in the cavities.

2. ) The method of claim 1 wherein the array is comprised of about 2 to about 10,000 cavities.

3. ) The method of claim 1 wherein the array is comprised of about 10,000 to about 1,000,000,000 cavities.

4. ) The method of claim 1 wherein the sensor is a field effect transistor.

5. ) The method of claim 1 wherein the sensor is comprised of single walled carbon nanotubes that are capable of acting as a field effect transistor.

6. ) The method of claim 3 or 4 wherein monitoring the cavities to detect changes in the reactants comprises detecting a change in current flow or a change in capacitance in a field effect transistor.

7. ) The method of claim 1 wherein the enzyme capable of extending a DNA molecule is a polymerase enzyme.

8. ) The method of claim 1 wherein the enzyme capable of deconstructing a DNA molecule is an exonuclease enzyme.

9. ) The method of claim 1 wherein attaching DNA to the surface of cavities comprises attaching a DNA probe capable of hybridizing to a sequence present in the sample of DNA molecule to the surface of the cavity and placing the sample of DNA into the cavity under conditions that allow DNA in the sample of DNA to hybridize to the probe DNA.

10. ) A method for determining the sequence of a sample of DNA to be sequenced comprising,

providing an array comprised of a plurality of cavities to hold reactants having a surface for attachment of DNA and a transparent section for detecting optical changes in a solution;

attaching DNA to the surfaces of the cavities so that statistically one DNA molecule is attached in one cavity;

terminating a primer strand of DNA hybridized to the DNA to be sequenced with a nuclease-resistant nucleotide;

providing reactants to the cavities comprising a nucleotide base, an enzyme capable of extending a DNA molecule, an enzyme capable of deconstructing a DNA molecule, and an indicator molecule capable of changing optical properties in response to a change in the reactants under conditions that allow DNA to be synthesized and deconstructed;

monitoring the cavities optically to detect changes in the reactants in the cavities;

repeating the elements of terminating the primer strand of DNA, providing reactants to the cavities, and monitoring the cavities at least one time; and

determining sequence information for the sample of DNA to be sequenced based on changes detected in the reactants in the cavities.

11. ) The method of claim 10 wherein the array is comprised of about 2 to about 10,000 cavities.

12. ) The method of claim 10 wherein the array is comprised of about 10,000 to about 1,000,000,000 cavities.

13. ) The method of claim 10 wherein the cavities have dimensions of less than about 10 μ

m.

14. ) The method of claim 10 wherein the enzyme capable of extending a DNA molecule is a polymerase enzyme.

15. ) The method of claim 10 wherein the enzyme capable of deconstructing a DNA molecule is an exonuclease enzyme.

16. ) The method of claim 10 wherein monitoring the cavities optically comprises determining a UV-vis absorbance or light emission.

17. ) The method of claim 10 wherein the transparent section comprises quartz, silica, or glass.

18. ) The method of claim 10 wherein attaching DNA to the surface of cavities comprises attaching a DNA probe capable of hybridizing to a sequence present in the sample of DNA molecule to the surface of the cavity and placing the sample of DNA into the cavity under conditions that allow DNA in the sample of DNA to hybridize to the probe DNA.

19. ) An array comprising a plurality of cavities for holding reactants, the cavities having a surface for attachment of DNA and an electronic sensor for detecting changes in a solution resulting from a chemical reaction and having statistically one DNA molecule of known sequence attached to the surface for attachment of DNA per cavity.

20. ) The method of claim 19 wherein the array is comprised of about 2 to about 10,000 cavities.

21. ) The method of claim 19 wherein the array is comprised of about 10,000 to about 1,000,000,000 cavities.

22. ) The array of claim 19 wherein the electronic sensor comprises a field effect transistor.

23. ) The array of claim 19 wherein the electronic sensor is comprised of single walled carbon nanotubes that are capable of acting as a field effect transistor.

24. ) The array of claim 19 also including a computer connected to the electronic sensors to analyze the electronic signals received from the field effect sensors.

25. ) The array of claim 24 also including an electronically controlled valve system connected to a fluid delivery system.

26. ) An array comprising a plurality of reaction cavities for holding reactants, the cavities having a surface for attachment of DNA and an optical sensor for detecting changes in a solution resulting from a chemical reaction and having statistically one DNA molecule of known sequence attached to the surface for attachment of DNA per reaction cavity.

27. ) The method of claim 26 wherein the array is comprised of about 2 to about 10,000 reaction cavities.

28. ) The method of claim 26 wherein the array is comprised of about 10,000 to about 1,000,000,000 reaction cavities.

29. ) The array of claim 26 wherein the optical sensor comprises a CMOS sensor or a photodiode.

30. ) The array of claim 26 also including a computer connected to the optical sensors to analyze the electronic signals received from the optical sensors.