Methods for detecting target analytes and enzymatic reactions

• US 7,622,294 B2
• Filed: 08/17/2004
• Issued: 11/24/2009
• Est. Priority Date: 03/14/1997
• Status: Expired due to Fees

• Current Assignee: Trustees of Tufts College
• Original Assignee: Trustees of Tufts College
• Inventors: Ballard, Karri Lynn, Walt, David R.
• Primary Examiner(s): YANG, NELSON C
• Application Number:
  US10/920,637
• Publication Number:
  US 20050130188A1
• Time in Patent Office: 1,925 Days
• Field of Search: None
• US Class Current: 435/287.1
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00524 in the shape of fiber bundles
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00704 integrated with the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/0074 : Biological products
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• 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: G01N 15/1456 : without spatial resolution of the texture or inner structure of the particle, e.g. processing of pulse signals
• CPC Class Codes: G01N 2015/1438 : Using two lasers in succession
• CPC Class Codes: G01N 2021/6441 : with two or more labels
• CPC Class Codes: G01N 2021/6484 : Optical fibres
• CPC Class Codes: G01N 2035/0097 : monitoring reactions as a function of time
• CPC Class Codes: G01N 21/6428 : Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6456 : Spatial resolved fluorescence measurements; Imaging
• CPC Class Codes: G01N 21/7703 : using reagent-clad optical fibres or optical waveguides using measurement of total internal reflection or attenuated total reflection G01N21/552; optical fibres or waveguides per se G02B
• CPC Class Codes: G01N 21/78 : producing a change of colour
• CPC Class Codes: G01N 2201/0826 : Fibre array at source, distributing
• CPC Class Codes: G01N 33/543 : with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/54313 : the carrier being characterised by its particulate form
• CPC Class Codes: Y02A 50/30 : Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
• CPC Class Codes: Y10S 435/808 : Optical sensing apparatus
• CPC Class Codes: Y10S 436/805 : Optical property

Abstract

A microsphere-based analytic chemistry system and method for making the same is disclosed in which microspheres or particles carrying bioactive agents may be combined randomly or in ordered fashion and dispersed on a substrate to form an array while maintaining the ability to identify the location of bioactive agents and particles within the array using an optically interrogatable, optical signature encoding scheme. A wide variety of modified substrates may be employed which provide either discrete or non-discrete sites for accommodating the microspheres in either random or patterned distributions. The substrates may be constructed from a variety of materials to form either two-dimensional or three-dimensional configurations. In a preferred embodiment, a modified fiber optic bundle or array is employed as a substrate to produce a high density array. The disclosed system and method have utility for detecting target analytes and screening large libraries of bioactive agents.

Claims

1. An array comprising:

(a) a population of beads comprising a first subpopulation of beads having attached nucleic acids and a second subpopulation of beads having attached enzymes, said beads of the first subpopulation being a different size from the beads of the second subpopulation; and

(b) a substrate having a surface comprising a random pattern of beads of said first subpopulation, said beads located at discrete sites, wherein each discrete site can have only a single associated bead from said first subpopulation and wherein said discrete sites further comprise beads from said second subpopulation.

2. The array of claim 1, wherein said nucleic acids comprise genomic DNA sequences.

3. The array of claim 1, wherein said nucleic acids comprise cDNA Sequences.

4. The array of claim 1, wherein said nucleic acids comprise portions of both single stranded sequence and double stranded sequence.

5. The array of claim 1, wherein said discrete sites are wells.

6. The array of claim 1, wherein said substrate is a fiber optic bundle comprising individual fibers and said wells are at a terminal end of said bundle.

7. The array of claim 1, wherein said first subpopulation of beads comprises beads having different attached nucleic acids.

8. The array of claim 1, wherein said second subpopulation of beads comprises beads having the same attached enzyme.

9. The array of claim 1, wherein said beads are from 0.5 to 5 microns in diameter.

10. The array of claim 1, further comprising a film formed over said array, wherein said film is permeable to aqueous species.

11. The array of claim 10, wherein said film comprises polyethylene glycol, polyacrylamide or polyhydroxymethyl methylacrylate.

12. The array of claim 1, wherein said nucleic acids have an unknown sequence.