Methods for concurrently processing multiple biological chip assays
Methods for concurrently processing multiple biological chip assays by providing a biological chip plate comprising a plurality of test wells, each test well having a biological chip having a molecular probe array; introducing samples into the test wells; subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a biological chip plate reader that interrogates the probe arrays to detect any reactions between target molecules and probes.
1 . A method for concurrently processing multiple biological chip assays comprising the steps of:
(a) providing a biological chip plate comprising a plurality of probe arrays and, surrounding the probe arrays, material resistant to the flow of liquid, thereby forming a plurality of test wells, each test well defining a space for the introduction of a sample;
(b) introducing into each test well test samples from a plurality of different patients, wherein each test sample contains target molecules;
(c) manipulating the biological chip plate with a fluid handling device that automatically performs steps to carry out reactions between target molecules in the test samples and probes in a plurality of the test wells; and
(d) interrogating the probe arrays of the biological chip plate with a biological chip plate reader to detect reactions between target molecules and probes in a plurality of the test wells to generate assay results.
2 . The method of claim 1 further comprising the step of processing the results with a computer.
3 . The method of claim 2 wherein the results are processed into an image with the intensity in each region of the image varying according to the binding affinity between targets and probes.
4 . The method of claim 1 wherein the probes are DNA or RNA molecules.
5 . The method of claim 4 wherein
(a) the reactions are hybridization of target molecules to probes; and
(b) the results provide information regarding the nucleotide sequence of the target molecule.
6 . The method of claim 5 wherein the assay is the detection or identification of a pathogenic organism.
7 . The method of claim 6 wherein the pathogenic organism is HIV.
8 . The method of claim 5 wherein the assay is the detection or identification of a human nucleic acid.
9 . The method of claim 8 wherein the assay is the detection of a human gene variant.
10 . The method of claim 9 wherein the human gene variant indicates the existence of, or predisposition to cystic fibrosis, diabetes, muscular dystrophy or cancer.
11 . The method of claim 1 further comprising controlling the temperature of the samples in the test wells and adding or removing fluids from the test wells at predetermined times.
12 . The method of claim 1 wherein the target molecule is tagged with a fluorescent marker, a chemiluminescent marker, a light scattering marker or a radioactive marker.
13 . The method of claim 12 wherein the marker is a fluorescent marker selected from the group consisting of fluorescein, rhodamine, or cyanine.
14 . The method of claim 12 wherein the fluid handling device and the biological chip plate reader comprise
(a) a confocal detection device having a monochromatic or polychromatic light source;
(b) optics for directing an excitation light from the light source at the substrate;
(c) a temperature controller for controlling temperature of the substrate during a reaction; and
(d) a detector for detecting fluorescence emitted by the targets in response to the excitation light.
15 . The method of claim 1 wherein the manipulating step comprises robotically controlling pipets for adding or removing fluids from the test wells at predetermined times.
16 . The method of claim 14 wherein the detector comprises a photomultiplier tube.
17 . The method of claim 14 wherein the interrogating step comprises focusing the excitation light to a point on the plate and determining the region from which the fluorescence originated.
18 . The method of claim 14 wherein the target is tagged with a fluorescent marker and the biological chip plate reader comprises a CCD array.
19 . The method of claim 1 wherein the probe arrays each have at least about 2500 features.
20 . The method of claim 1 wherein the probe arrays each have at least about 50,000 features.
21 . The method of claim 1 wherein said chip plate is made by the steps of mating a wafer comprising a plurality of probe arrays to an array of open ended wells.
22 . The method of claim 1 wherein the interrogating step comprises the steps of:
(a) directing excitation light through a bottom surface of said plate; and
(b) detecting where targets bound on said probe arrays.
23 . The method of claim 1 wherein the interrogating step comprises determining the on- or off-rates of binding between target molecules in a sample and probes.
24 . The method of claim 1 wherein the probe arrays are produced by light-directed probe synthesis.
25 . The method as recited in claim 24 wherein said arrays of probes are made by repeating the steps of:
(a) selectively directing light at said surface to remove photoremovable protecting groups; and
(b) selectively coupling monomers to said surface.
26 . The method of claim 24 wherein the chip comprises a contiguous substrate that comprises a contiguous surface a arrays are attached to the contiguous surface.
27 . The method of claim 1 wherein each probe array is about 0.25 cm 2 .
28 . The method of claim 1 wherein each probe array is about 1 cm 2 .
29 . The method of claim 1 wherein the probe arrays comprise features of about 100 microns on a side.
30 . The method of claim 1 wherein the probe arrays comprise features of about 20 microns on a side.
31 . The method of claim 1 wherein the chip comprises a contiguous substrate that comprises a contiguous surface and the plurality of probe arrays are attached to the contiguous surface.