Chemically induced optical signals and DNA sequencing

Patent metadata

Field	Value
Publication number	US-9671558-B2
Application number	US-45930909-A
Country	US
Kind code	B2
Filing date	Jun 30, 2009
Priority date	Jun 30, 2009
Publication date	Jun 6, 2017
Grant date	Jun 6, 2017

Abstract

Methods for sequencing nucleic acids are presented. Sequencing is accomplished through the chemical amplification of the products of DNA synthesis and the detection of the chemically amplified products. In embodiments of the invention, a substrate is provided having a plurality of molecules of DNA to be sequenced attached and a plurality of molecules capable of chelating pyrophosphate ions attached, the DNA molecules to be sequenced are primed, and a next complementary nucleotide is incorporated and excised a plurality of times leading to the buildup of pyrophosphate ions locally around the DNA molecule to be sequenced. Pyrophosphate ions are captured by the substrate-attached chelators and optically detected to determine the identity of the next complementary nucleic acid in the DNA molecule to be sequenced.

First claim

The invention claimed is:

1. A device comprising:
a substrate, included in a waveguide, wherein the substrate has a surface that comprises both: (a) a plurality of attachment sites for nucleic acid molecules to be sequenced, and (b) a plurality of attached molecules capable of chelating a pyrophosphate ion,
an optical system comprising a light source, a light source control, and an image detector,
an electronics system operably coupling a computer to the optical system,
a function layer having a first index of refraction, and
a layer, included in the waveguide and directly contacting the function layer, having a second index of refraction greater than the first index of refraction,
wherein the computer is capable of receiving, storing, and processing data from the electronics system in order to assemble the sequence of a nucleic acid molecule to be sequenced,
wherein the light source is positioned so light from the light source is directed: (a)(i) into and orthogonal to a first side of the waveguide, and (a)(ii) parallel to a second side of the waveguide;
wherein the second side of the waveguide includes the surface of the substrate.

2. The device of claim 1 comprising:
an inlet oriented and proportioned to fluidly couple with fluid from a fluid delivery system;
wherein the substrate is a planar waveguide and the surface fluidly couples to the inlet to receive and directly contact the fluid.

3. The device of claim 2 wherein the planar waveguide comprises SiO 2 .

4. The device of claim 2 also comprising the fluid delivery system, wherein the fluid delivery system is comprised of a plurality or reservoirs capable of containing a plurality of solutions and a plurality of outlets from the plurality of reservoirs capable of delivering fluids to the surface of the substrate.

5. The device of claim 2 wherein the electronics system is capable of causing a solution from a reservoir to be supplied to the surface of the substrate and wherein the computer is capable of directing the electronics system to supply a solution from a reservoir to the surface of the substrate.

6. A device comprising:
a substrate including a zero mode waveguide having a surface wherein the surface comprises a plurality of attachment sites for nucleic acid molecules to be sequenced and a plurality of attached molecules capable of chelating a pyrophosphate ion and wherein the surface comprises a patterned metal layer wherein the patterned metal layer has a thickness of between 1 nm and 100 nm,
an optical system comprising a light source, a light source control, and an image detector,
an electronics system operably coupling a computer to the optical system, and
the computer capable of receiving, storing, and processing data from the electronics system in order to assemble the sequence of a nucleic acid molecule to be sequenced;
wherein the patterned metal layer comprises holes in the metal layer, the holes have diameters that are less than a wavelength of light from the light source, and the wavelength of light is capable of exciting a molecule for which an emission is to be detected by the image detector.

7. The device of claim 6 wherein the attachment sites for nucleic acid molecules to be sequenced are located within the holes.

8. The device of claim 7 wherein the metal layer comprises at least one of is comprised of silver, gold, and copper.

9. The device of claim 7 also comprising a fluid delivery system, wherein the fluid delivery system is comprised of a plurality or reservoirs capable of containing a plurality of solutions and a plurality of outlets from plurality of reservoirs capable of delivering fluids to the surface of the substrate.

10. The device of claim 9 wherein the electronics system is capable of causing a solution from a reservoir to be supplied to the surface of the substrate and wherein the computer is capable of directing the electronics system to supply a solution from a reservoir to the surface of the substrate.

11. A device comprising:
a substrate that is capable of functioning as a plasmonic waveguide having a surface wherein the surface comprises a plurality of attachment sites for nucleic acid molecules to be sequenced and a plurality of attached molecules capable of chelating a pyrophosphate ion and wherein the surface comprises a patterned metal layer having holes and the attachment sites for nucleic acid molecules and the plurality of attached molecules capable of chelating a pyrophosphate ion are located within the holes,
an optical system comprising a light source, a light source control, and an image detector,
an electronics system operably coupling a computer to the optical system, and the computer capable of receiving, storing, and processing data from the
electronics system in order to assemble the sequence of a nucleic acid molecule to be sequenced.

12. The device of claim 11 wherein the holes in the patterned metal layer have a dimension that is larger than a wavelength of light from the light source wherein the wavelength of light is capable of exciting a molecule for which an emission is to be detected by the image detector.

13. The device of claim 12 wherein the metal layer comprises at least one of silver, gold, and copper.

14. The device of claim 12 also comprising a fluid delivery system, wherein the fluid delivery system is comprised of a plurality or reservoirs capable of containing a plurality of solutions and a plurality of outlets from the plurality of reservoirs capable of delivering fluids to the surface of the substrate.

15. The device of claim 14 wherein the electronics system is capable of causing a solution from a reservoir to be supplied to the surface of the substrate and wherein the computer is capable of directing the electronics system to supply a solution from a reservoir to the surface of the substrate.

16. The device of claim 2 wherein the molecules capable of chelating a pyrophosphate ion comprise a detectable label.

17. The device of claim 7 wherein the molecules capable of chelating a pyrophosphate ion comprise a detectable label.

18. The device of claim 12 wherein the molecules capable of chelating a pyrophosphate ion comprise a detectable label.

19. The device of claim 2 , wherein the function layer includes the surface of the substrate.

20. The device of claim 19 , wherein the plurality of attached molecules capable of chelating a pyrophosphate ion each include a linker.

Assignees

• Su Xing
• Wang Liming
• Liu Jianquan
• Wu Kai
• Intel Corp

Inventors

• Su Xing
• Wang Liming
• Liu Jianquan
• Wu Kai

Classifications

• G02B6/1221 Primary

  made from organic materials · CPC title

• C12Q1/6874

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• C12Q2563/107

  fluorescence · CPC title

• C12Q2565/607

  being a sensor, e.g. electrode · CPC title

• C12Q2527/125

  Specific component of sample, medium or buffer · CPC title