Spatially addressable combinatorial chemical arrays in encoded optical disk format

• US 7,094,609 B2
• Filed: 09/19/1997
• Issued: 08/22/2006
• Est. Priority Date: 09/20/1996
• Status: Expired due to Fees

• Current Assignee: Vindur Technologies, Inc.
• Original Assignee: Burstein Technologies, Inc., Nagaoka & Co., Ltd.
• Inventors: Demers, James Paul
• Primary Examiner(s): Ponnaluri, Padmashri
• Application Number:
  US09/269,092
• Publication Number:
  US 20020058242A1
• Time in Patent Office: 3,259 Days
• Field of Search: 436/518, 436/501, 436/45, 436/164, 436/165, 435/6, 435/DIG.43, 435/DIG.44, 435/DIG.45, 435/4, 435/7.1, 435/DIG.49, 435/DIG.22, 435/DIG.34, 435/DIG.2, 530/333, 530/334, 536/25.3, 235/454
• US Class Current: 436/518
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00436 Maskless processes
• CPC Class Codes: B01J 2219/00441 using lasers
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00599 Solution-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/0072 : Organic compounds
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 50/08 : Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creation; Particular methods of cleavage from the liquid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 33/53 : Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/54353 : with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: Y10T 436/144444 : Glucose

Abstract

A method for preparing very large spatially-addressable arrays of chemical compounds by light-directed synthesis is provided, wherein the light is provided by a laser and the compounds are arrayed on a rotating disc in a CD-ROM format. A method for assaying the resulting array with a CD-ROM mechanism is also provided.

Claims

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.

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.

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.

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.