Electronic detection of hybridization on nucleic acid arrays

• US 6,403,317 B1
• Filed: 03/24/2000
• Issued: 06/11/2002
• Est. Priority Date: 03/26/1999
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Anderson, Rolfe C.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): FORMAN, BETTY J
• Application Number:
  US09/535,142
• Time in Patent Office: 809 Days
• Field of Search: 435/6, 435/288.7, 435/287.2, 422/68.1, 422/82.01, 422/82.05, 422/82.12
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2527/101 Temperature
• CPC Class Codes: C12Q 2565/107 Alteration in the property of hybridised versus free label oligonucleotides
• CPC Class Codes: G01N 15/01 specially adapted for biological cells, e.g. blood cells investigating sedimentation of particle suspensions in blood G01N15/05
• CPC Class Codes: G01N 15/1031 by measuring electrical or magnetic effects
• CPC Class Codes: G01N 21/1717 with a modulation of one or more physical properties of the sample during the optical investigation, e.g. electro-reflectance
• CPC Class Codes: G01N 25/4846 for a motionless, e.g. solid sample

Abstract

A method of detecting locations on a nucleic acid probe array at which hybridization occurs between targets in a fluid sample and nucleic acid probes disposed on a surface of the nucleic acid probe array, comprising: measuring the temperature at a plurality of locations on the surface of the nucleic acid probe array; applying an oscillating level of energy to the surface of the nucleic acid probe array, thereby causing the temperature at the surface of the nucleic acid probe array to oscillate; and detecting a decreased range of temperature oscillation at least one of the plurality of locations on the nucleic acid probe array, thereby indicating an increased heat capacity caused by latent heat of hybridization between at least one target in the fluid sample and at least one nucleic acid probe disposed on a surface of the nucleic acid probe array.

Claims

1. A method of detecting locations on a nucleic acid probe array at which hybridization occurs between targets in a fluid sample and nucleic acid probes attached to a surface of the nucleic acid probe array, comprising:

measuring the temperature at a plurality of locations on the surface of the nucleic acid probe array;

applying energy to the surface of the nucleic acid probe array, thereby causing the temperature at the surface of the nucleic acid probe array to increase; and

detecting a decrease in the rate of temperature change at least one of the plurality of locations, where hybridization has occurred, compared to the rate of temperature change at another of the plurality of locations, where hybridization has not occurred, on the nucleic acid probe array, said decrease being due to an increased heat capacity caused by hybridization between at least one target in the fluid sample and at least one nucleic acid probe disposed on a surface of the nucleic acid probe array at said at least one hybridization location.

3. The method of claim 1 or 2 including an array of heaters, each heater being disposed under a patch of probes.

4. The method of claim 3, further comprising:

adjusting the temperature at each patch of probes to a temperature approximately equal to the temperature at which hybridization occurs between the patch of probes and the targets.

5. The method of claim 1 or 2 further comprising:

providing an optically absorbing layer under the probe array;

providing a thermal insulation layer under the optically absorbing material; and

providing a substrate under the thermal insulation layer.

6. The method of claim 5, wherein the substrate comprises a material selected from the group consisting of a ceramic, silicon or glass.

7. The method of claim 5, wherein the optically absorbing layer comprises a thin nickel film.

8. The method of claim 1 or 2, wherein said measuring includes using an infrared scanner to measure the temperature at a plurality of locations on the surface of the nucleic acid probe array.

9. The method of claim 1, wherein applying energy to the surface of the nucleic acid probe array is accomplished by at least one heater disposed under the nucleic acid probe array.

10. The method of claim 9, wherein the at least one heater comprises an array of heaters, each heater being disposed under a patch of probes.

11. The method of claim 10, further comprising:

adjusting the temperature at each patch of probes to a temperature approximately equal to the temperature at which hybridization occurs between the patch of probes and the targets.

14. The method of claim 1, 2 or 12, wherein said measuring includes detecting a shift in double-layer capacitance resulting from a change in a dielectric constant.

15. The method of claim 1, 2 or 12, wherein said measuring includes detecting a shift in a point of zero charge in a semiconductor electrolyte interface.

16. The method of claim 1, 2 or 12, wherein said measuring includes detecting a shift in the zeta potential of an insulating layer.

2. A method of detecting locations on a nucleic acid probe array at which hybridization occurs between targets in a fluid sample and nucleic acid probes attached to a surface of the nucleic acid probe array, comprising:

measuring the temperature at a plurality of locations on the surface of the nucleic acid probe array;

decreasing the temperature of the surface of the nucleic acid probe array; and

detecting a decrease in the rate of temperature change at least one of the plurality of locations, where hybridization has occurred compared to the rate of temperature change at another of the plurality of locations, where hybridization has not occurred, on the nucleic acid probe array, said decrease being due to an increased heat capacity caused by hybridization between at least one target in the fluid sample and at least one nucleic acid probe disposed on a surface of the nucleic acid probe array at said at least one hybridization location.

12. A method of detecting locations on a nucleic acid probe array at which hybridization occurs between targets in a fluid sample and nucleic acid Probes attached to a surface of the nucleic acid probe array, comprising:

measuring the temperature at a plurality of locations on the surface of the nucleic acid probe array;

applying an oscillating amount of energy to the surface of the nucleic acid probe array including directing the output of a first laser at the surface of the nucleic acid probe array and directing the output of a second laser at the surface of the nucleic acid probe array, wherein the output of the first laser is greater than the output of the second laser, thereby causing the temperature at the surface of the nucleic acid probe array to oscillate; and

detecting a decreased range of temperature oscillation at least one of the plurality of locations, where hybridization has occurred, compared to a range of temperature oscillation at another of the plurality of locations, where hybridization has not occurred, on the nucleic acid probe array, said decreased range being due to an increased heat capacity caused by hybridization between at least one target in the fluid sample and at least one nucleic acid probe disposed on a surface of the nucleic acid probe array at said at least one hybridization location.

13. The method of claim 12, wherein the first laser is adapted to control the average temperature at the probe array, and the second laser is adapted to fine tune the temperature at the probe array.