US5653939A — Optical and electrical methods and apparatus for …

Claim 1

Independent Claim 152 words

A method for testing a sample substance for the presence of target nucleic acids comprising the steps of: a) forming an array of test sites in multiple locations, each site having oligonucleotide probes formed therein of known binding characteristics and wherein the probes in each test site differ from the probes in other test sites in a known predetermined manner, such that the test site location of probes and their binding characteristics are also known; b) applying the sample substance to the test sites; and c) detecting a change in the electromagnetic properties of the test sites resulting from the binding of target nucleic acid within the sample substance to probes in the test sites by detection circuitry coupled to individual test sites to determine which target nucleic acid have bonded to a test site; whereby the presence of a multiplicity of different target nucleic acids in the sample can be detected.

Claim 2

Independent Claim 152 words

A method for testing a sample substance for the presence of target nucleic acids comprising the steps of: a) forming an array of test sites in multiple locations, each site having oligonucleotide probes formed therein of known binding characteristics and wherein the probes in each test site differ from the probes in other test sites in a known predetermined manner, such that the test site location of probes and their binding characteristics are also known; b) applying the sample substance to the test sites; and c) detecting a change in the electromagnetic properties of the test sites resulting from the binding of target nucleic acid within the sample substance to probes in the test sites by detection circuitry coupled to individual test sites to determine which target nucleic acid have bonded to a test site; whereby the presence of a multiplicity of different target nucleic acids in the sample can be detected.

Claim 3

Dependent Claim 104 words

The method of claim 1 wherein a test signal is applied to the test sites which is an electro-magnetic signal and forming said array comprises the steps of: a) forming a first layer on a substrate; b) forming a second layer on the first layer; c) forming openings in the second layer into the first layer exposing a portion of the first layer; and d) forming a pair of electrodes, one electrode on the first layer on the exposed portions in the openings and another electrode on the second layer adjacent to the openings, and wherein said test signal is applied to the electrodes.

Claim 4

Dependent Claim 53 words

The method of claim 2 wherein forming said pair of electrodes comprises the steps of depositing metallization on the second layer after the openings are formed; which metallization forms an upper electrode on the surface of the second layer between openings and a lower electrode on the exposed portions of the first layer.

Claim 5

Dependent Claim 26 words

The method of claim 3 wherein the substrate is formed of silicon, and the first layer and second layer are formed of a silicon based dielectric.

Claim 6

Dependent Claim 35 words

The method of claim 4 wherein the first and second layers are SiO 2 and Si 3 N 4 , respectively, and the metallization comprises Al, Ti, Pt, W, Ta and their silicides or Au.

Claim 7

Dependent Claim 19 words

The method of claim 1 wherein said step of detecting comprises detecting the dielectric properties of the test site.

Claim 8

Dependent Claim 23 words

The method of claim 1 wherein a test signal is applied to the test sites which is a pulsed or varying frequency signal.

Claim 9

Independent Claim 25 words

The method of clam 1 wherein each test site is formed with a resonant structure which is resonant in a frequency range of electrical signals.

Claim 10

Independent Claim 25 words

The method of clam 1 wherein each test site is formed with a resonant structure which is resonant in a frequency range of electrical signals.

Claim 11

Dependent Claim 23 words

The method of claim 8 wherein said detecting step comprises detecting changes in the Q or the resonant frequency of the resonant structure.

Claim 12

Dependent Claim 16 words

The method of claim 1 wherein said sample substance is in a solution or a gel.

Claim 13

Dependent Claim 78 words

Apparatus for synthesizing molecular probes in situ comprising: a) an array of test sites each site containing precursor molecules to be reacted; b) an array of resistors disposed adjacent to the test site array with a respective resistor located in proximity to a respective test site; and c) coupling means for coupling a respective resistor to an electrical source for heating a respective resistor to induce a thermal reaction for synthesis of molecules in a respective test site.

Claim 14

Dependent Claim 78 words

Apparatus for synthesizing molecular probes in situ comprising: a) an array of test sites each site containing precursor molecules to be reacted; b) an array of resistors disposed adjacent to the test site array with a respective resistor located in proximity to a respective test site; and c) coupling means for coupling a respective resistor to an electrical source for heating a respective resistor to induce a thermal reaction for synthesis of molecules in a respective test site.

Claim 15

Dependent Claim 19 words

The apparatus of claim 11 wherein the test site array and resistor array are formed as an integrated structure.

Claim 16

Dependent Claim 46 words

Apparatus for synthesizing molecular structures in situ comprising: a) an array of test sites each site containing precursor molecules to be reacted; and b) each test site containing electrodes coupled to a voltage source for inducing a reaction to synthesize molecules in a respective test site.

Claim 17

Dependent Claim 46 words

Apparatus for synthesizing molecular structures in situ comprising: a) an array of test sites each site containing precursor molecules to be reacted; and b) each test site containing electrodes coupled to a voltage source for inducing a reaction to synthesize molecules in a respective test site.

Claim 18

Dependent Claim 15 words

The apparatus of claim 13 wherein the array and electrodes are formed in integrated structures.

Claim 19

Independent Claim 69 words

A method for synthesizing a plurality of different known molecular structures on an array of test sites comprising: a) providing an array of test sites; b) providing a source of chemical reactants disposed adjacent the test sites; c) providing electrodes associated with respective test sites; and d) applying a potential to a respective electrode to synthesize said different known molecular structures at said different known sites in the array.

Claim 20

Independent Claim 69 words

A method for synthesizing a plurality of different known molecular structures on an array of test sites comprising: a) providing an array of test sites; b) providing a source of chemical reactants disposed adjacent the test sites; c) providing electrodes associated with respective test sites; and d) applying a potential to a respective electrode to synthesize said different known molecular structures at said different known sites in the array.

Claim 21

Dependent Claim 94 words

Apparatus for enhancing hybridization between a synthesized probe and a target molecule comprising: a) an array of test sites each site containing a plurality of probes, each test site having probes of known binding characteristics, and wherein the probes in each test site differ from the probes in other test sites in a known predetermined manner; b) an electrode associated with each site; c) a source of target molecules applied to said sites; and d) a voltage source for applying a potential to a respective electrode for attracting said target molecules to said probes.

Claim 22

Dependent Claim 94 words

Apparatus for enhancing hybridization between a synthesized probe and a target molecule comprising: a) an array of test sites each site containing a plurality of probes, each test site having probes of known binding characteristics, and wherein the probes in each test site differ from the probes in other test sites in a known predetermined manner; b) an electrode associated with each site; c) a source of target molecules applied to said sites; and d) a voltage source for applying a potential to a respective electrode for attracting said target molecules to said probes.

Claim 23

Dependent Claim 11 words

The method of claim 6 wherein the dielectric property is permittivity.

Claim 24

Dependent Claim 14 words

The method of claim 1 wherein the sample substance is in a solid state.

Claim 25

Dependent Claim 28 words

The method of claim 8 wherein the resonant structure is a transmission line and changes in phase or amplitude of a signal propagated on the line are detected.

Claim 26

Independent Claim 120 words

A method for determining the presence of molecular structures within a sample substance comprising: a) forming an array of test sites having specific known oligonucleotide probes formed therein selected to bind with said structures of known binding characteristics, each site having oligonucleotide probes which bind to a different structure and wherein the location of the sites containing specific known oligonucleotide probes is also known; b) dispensing a sample substance into a test site; c) generating radiation through the test sites; and d) detecting, by detection circuitry coupled to individual test sites of the array, the difference in the radiation which is absorbed by the respective test sites to determine the presence of the structures which are bonded to a probe.

Claim 27

Independent Claim 120 words

A method for determining the presence of molecular structures within a sample substance comprising: a) forming an array of test sites having specific known oligonucleotide probes formed therein selected to bind with said structures of known binding characteristics, each site having oligonucleotide probes which bind to a different structure and wherein the location of the sites containing specific known oligonucleotide probes is also known; b) dispensing a sample substance into a test site; c) generating radiation through the test sites; and d) detecting, by detection circuitry coupled to individual test sites of the array, the difference in the radiation which is absorbed by the respective test sites to determine the presence of the structures which are bonded to a probe.

Claim 28

Dependent Claim 30 words

The method of claim 20 wherein the difference is detected by an array of detectors formed of charge-coupled devices which are optically coupled to the test sites of the array.

Claim 29

Dependent Claim 23 words

The method of claim 20 wherein the difference is detected by an array of detectors formed integral with the array of test sites.

Claim 30

Dependent Claim 23 words

The method of claim 20 wherein the difference is detected by an array of detectors formed separate from the array of test sites.

Claim 31

Dependent Claim 30 words

The method of claim 23 wherein the array of detectors is aligned with the array of test sites and radiation is projected through the test sites onto the detector array.

Claim 32

Dependent Claim 17 words

The method of claim 24 wherein the radiation is in the form of photons, or radioactive particles.

Claim 33

Dependent Claim 23 words

The method of claim 20 wherein the radiation is generated within the test sites by a radioactive, chemical, thermal, chemiluminescent, or luminescent reaction.

Claim 34

Dependent Claim 18 words

The method of claim 20 wherein the detectors detect thermal energy occurring when a bonding reaction takes place.

Claim 35

Independent Claim 96 words

A method for attaching probes to a test site formed in a substrate comprising the steps of: a) forming test sites in a substrate; b) forming an adhesive material in the test site which material enables probes to attach to the test sites; c) forming a coating over the adhesive material; d) contacting the coating with a coating-removal material while selectively initiating a reaction at a selected site which removes the coating at the selected site; and e) contacting the site in which the coating has been removed with probes which adhere to the adhesive material.

Claim 36

Independent Claim 96 words

A method for attaching probes to a test site formed in a substrate comprising the steps of: a) forming test sites in a substrate; b) forming an adhesive material in the test site which material enables probes to attach to the test sites; c) forming a coating over the adhesive material; d) contacting the coating with a coating-removal material while selectively initiating a reaction at a selected site which removes the coating at the selected site; and e) contacting the site in which the coating has been removed with probes which adhere to the adhesive material.

Claim 37

Dependent Claim 52 words

The method of claim 28 wherein the probes are presynthesized and the test sites consist of wells, the adhesive material is an epoxide, the coating is formed by hydrolyzing the epoxide, the coating-removal material is an acetate alcohol solution and the reaction is initiated at a selected site by heating the site.

Claim 38

Dependent Claim 25 words

The method of claim 28 wherein the reaction is initiated by selectively energizing resistors formed adjacent the test sites to heat the selected test sites.

Claim 39

Dependent Claim 19 words

The method of claim 30 wherein non-selected test sites are maintained at a temperature above the desired reaction temperature.

Claim 40

Dependent Claim 16 words

The method of claim 28 wherein the reaction is initiated by irradiating selected sites with light.

Claim 41

Dependent Claim 21 words

The method of claim 32 wherein the light is in the visible or ultraviolet wavelength range and a photochemical reaction occurs.

Claim 42

Dependent Claim 23 words

The method of claim 32 wherein the light originates from a laser which is scanned from site to site to initiate the reaction.

Claim 43

Dependent Claim 18 words

The method of claim 32 wherein the light induces local heating of the site to initiate a reaction.

Claim 44

Dependent Claim 20 words

The method of claim 32 wherein the light is generated by a light valve which projects light onto selected sites.

Claim 45

Dependent Claim 19 words

The method of claim 32 wherein the light source is a light valve for projecting light onto selected sites.

Claim 46

Dependent Claim 22 words

The apparatus of claim 13 wherein the voltage source provides a reverse biased potential applied to the electrodes subsequent to molecule synthesis.

Claim 47

Dependent Claim 27 words

The apparatus of claim 16 wherein the voltage source provides a reverse biased potential applied to the electrodes to aid in the removal of unhybridized target molecules.

Annuity Stage	Window Opens	Payment Deadline	Surcharge Period Until	Estimated Fee	Status
3.5 Years (Year 4)	2000-08-04	2001-02-03	2001-08-05	$2000.00	Window Closed / Lapsed
7.5 Years (Year 8)	2004-08-04	2005-02-03	2005-08-05	$3760.00	Window Closed / Lapsed
11.5 Years (Year 12)	2008-08-04	2009-02-03	2009-08-05	$7700.00	Window Closed / Lapsed

Optical and electrical methods and apparatus for molecule detection

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