Spatially addressable combinatorial chemical arrays in encoded optical disk format

1. A method conducting an optical inspection of an array of synthesis sites to identify one or more synthesis sites where an analyte is bound, said method comprising the steps of:

providing a mechanism comprising a laser and laser detector;

providing an optical disc which includes encoded information in a form that is readable by the mechanism, said optical disc further including an array of synthesis sites where each of said synthesis sites includes chemically reactive, reactive compounds which are capable of binding selectively to an analyte and wherein said mechanism provides a laser beam which is used to optically inspect said synthesis sites and includes a sample beam and a reference beam and where said sample beam is reflected from or transmitted through said synthesis site and said reference beam is reflected from or transmitted through a location on said disc adjacent to said synthesis site;

using said mechanism to conduct an optical inspection of said array of synthesis sites to provide identification of which synthesis sites contain said analyte;

reading said encoded information with said mechanism and

conducting said optical inspection in response to encoded information that was read.

2. A method of conducting an optical inspection of an array of synthesis sites to identify one or more synthesis sites where an analyte is bound, said method comprising the steps of:

providing a mechanism comprising a laser and a laser detector;

providing an optical disc which includes encoded information in a form that is readable by the mechanism, said optical disc further including an array of synthesis sites and a reflective surface located below said synthesis sites and where each of said synthesis sites includes chemically reactive, activated compounds which are capable of binding selectively to an analyte, and wherein said mechanism provides a laser beam which is used to optically inspect said synthesis sites;

using said mechanism to conduct an optical inspection of said array of synthesis sites to provide identification of which synthesis sites contain said analyte where said optical inspection includes the steps of: directing said laser beam through said synthesis site to provide an altered laser beam which contacts said reflective surface; reflecting said altered laser beam back from said reflective surface through said synthesis site to form a reflected signal beam; and detecting one or more properties of said reflected signal beam;

reading said encoded information with said mechanism and

conducting said optical inspection in response to encoded information that was read.

3. A method of conducting an optical inspection of an array of synthesis sites to identify one or more synthesis sites where an analyte is bound, said method comprising the steps of:

providing a mechanism comprising a laser and a laser detector;

providing an optical disc which includes encoded information in a form that is readable by the mechanism, said optical disc further including an array of synthesis sites where each of said synthesis sites includes chemically reactive, activated compounds which are capable of binding selectively to an analyte and wherein said mechanism provides a laser beam which is used to optically inspect said synthesis sites;

using said mechanism to conduct an optical inspection of said array of synthesis sites to provide identification of which synthesis sites contain said analyte, wherein said optical inspection includes, the steps of directing said laser beam through said synthesis site to provide an altered laser beam which is transmitted through said synthesis site and detecting one or more properties of said altered laser beam which has been transmitted through said synthesis site;

reading said encoded information with said mechanism and

conducting said optical inspection in response to encoded information that was read.

4. The method of conducting an optical inspection of an array of synthesis sites according to anyone of claims 1 through 3 wherein said analyte includes a polypeptide, protein, nucleic acid or oligonucleotide.

5. The method according to any one of claims 1 through 3 which includes the additional step of using said mechanism to conduct light-directed synthesis in at least a portion of at said synthesis sites.

6. The method of conducting an optical inspection of an array of synthesis sites according to any one of claims 1 through 3 wherein each of said synthesis sites covers an area on said optical disc of between 100 and 400 square microns.

7. The method of conducting and optical inspection of an array of synthesis sites according to any one of claims 1 through 3 wherein said analyte includes a label selected from the group of fluorescent labels, metal labels and dye labels.

8. The method of conducting an optical inspection of an array of synthesis sites according to any one of claims 1 through 3 wherein said analyte is capable of altering one or more properties of said laser beam, said properties being selected from the group of intensity, polarization angle, wavelength and phase.

9. A method of detecting the presence of an analyte, comprising the steps of:

providing a mechanism comprising a laser and a laser detector;

providing an optical disc with encoded information in a form that is readable by the mechanism and an array of synthesis sites wherein each of said sites includes chemically reactive, activated compounds which are capable of binding selectively to an analyte, said mechanism including a laser beam capable of synthesis and optical inspection of said sites;

exposing at least some of the array of synthesis sites to a substance of interest, wherein said substance of interest may comprise an analyte;

conducting an optical inspection of said sites using said mechanism, to inspect them for the binding of selected analytes to said synthesis sites;

reading said encoded information with said mechanism and

conducting said optical inspection in response to encoded information that was read.