Gradient resolved information platform

• US 7,183,050 B2
• Filed: 04/18/2002
• Issued: 02/27/2007
• Est. Priority Date: 04/18/2001
• Status: Expired due to Fees

• Current Assignee: Ulrich J. Krull
• Original Assignee: Ulrich J. Krull
• Inventors: Krull, Ulrich J.
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US10/126,504
• Publication Number:
  US 20030055233A1
• Time in Patent Office: 1,776 Days
• Field of Search: 435/6, 435/174, 435/283.1, 435/287.2, 435/287.9, 536/23.1, 536/24.3
• US Class Current: 435/6.11
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00524 in the shape of fiber bundles
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00545 Colours
• CPC Class Codes: B01J 2219/00574 radioactive
• CPC Class Codes: B01J 2219/00576 fluorophore
• 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 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00628 Ionic
• 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 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• 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 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• 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: C12Q 2527/137 : Concentration of a component of medium
• CPC Class Codes: C12Q 2527/143 : Concentration of primer or probe
• CPC Class Codes: C12Q 2527/15 : Gradients
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: Y10S 977/924 : using nanostructure as support of dna analysis

Abstract

Methods and devices for the detection and identification in a sample of one or more target molecules which bind to nucleic acid probe molecules are provided. The method includes contacting the sample with a surface that is coated with one or more gradients of nucleic acid or nucleic acid analog probe molecules that bind target molecules in the sample. Gradients are formed by varying a physical, structural or functional property of the probes on the surface; for example, the density of probe molecules bound to the surface. The coating layer or immobilization layer in which the gradient is formed is preferably continuous Determination of the location, speed and/or extent of hybridisation of a nucleic acid on a gradient surface is useful to identify target molecules bound to probes and/or to quantitatively measure the amount of the target in a sample.

Claims

1. A hybridization platform comprising:

a planar support; and

an immobilized layer of single stranded nucleic acids or nucleic acid analogs formed on the surface of the planar support;

wherein the immobilized layer is formed as either a) a continuous layer on the surface or b) as discrete regions on the surface;

the nucleic acids or nucleic acid analogs being arranged as the continuous layer, or as each region, such that the one or more parameters selected from the density, sequence, orientation or structure of the nucleic acid or nucleic acid analogs are spatially varied as a continuum in the continuous layer or in each region in one or both of a first and second dimension across the surface of the planar support so as to form at least one gradient of the one or more parameters within the continuous layer or each region; and

the one or more selected parameters includes the density of the nucleic acid or nucleic acid analogs.

2. The hybridization platform of claim 1 which comprises a first gradient and a second gradient, wherein the first gradient is formed by spatially varying the density of the nucleic acids or nucleic acid analogs.

3. The hybridization platform of claim 2 wherein the immobilized layer further comprises polyelectrolyte immobilized to the surface of the planar support such that a further gradient is formed by spatially varying the concentration of polyelectrolyte.

4. The hybridization platform of claim 2, wherein the at least on gradient spans an average nearest neighbour separation of from about 2 mm to over 40 nm.

5. The hybridization platform of claim 2 wherein the planar support is fused silica, quartz, silicon, glass, a plastic, a metal, a transparent electrode, a ceramic, a semiconductor, a conductive form of carbon, paper, a conductive polymer, or a waveguide operating in either the evanescent mode or direct mode of excitation.

6. The hybridization platform of claim 5 wherein the at least one gradient is formed by dip-casting, through gradients of light activation, by spraying, rolling, capping, sequence annealing, sequence degradation, sequence extension or combinations thereof.

7. The hybridization platform of claim 6 wherein the nucleic acids or nucleic acid analogs are immobilized to the surface by adsorption, absorption, ionic bonding, covalent bonding, avidin-biotin, or thiol-gold interactions.

8. The hybridization platform of claim 7 wherein the nucleic acids or nucleic acid analogs are immobilized to the surface by covalent bonding.

9. The hybridization platform of claim 5 wherein the planar support is a waveguide, operating in either the evanescent mode or direct mode of excitation.

10. The hybridization platform of claim 2 wherein the first and second gradients are formed in orthogonal dimensions of the surface.

11. The hybridization platform of claim 2 wherein the second gradient is formed by varying the sequence of the nucleic acids or nucleic acid analogs.

12. The hybridization platform of claim 2 wherein the immobilized layer further comprises detectable labels that indicate binding of target molecules to the nucleic acids or nucleic acid analogs.

13. The hybridization platform of claim 2 further comprising detectable labels bound to the nucleic acids or nucleic acid analogs.

14. The hybridization platform of claim 13 wherein the detectable labels are fluorescent labels tethered to the nucleic acid or nucleic acid analogs.

15. The hybridization platform of claim 2 further comprising fluorescent labels immobilized to the surface.

16. The hybridization platform of claim 2 further comprising a further gradient formed by varying the density of detectable labels tethered to the nucleic acids or nucleic acid analogs.

17. The hybridization platform of claim 16 wherein the detectable labels are fluorescent molecules.

18. The hybridization platform of claim 2 further comprising a reference region in the at least one gradient.

19. The hybridization platform of claim 2 wherein the second gradient is formed by varying the length of the nucleic acids or nucleic acid analogs in the immobilized layer.

20. The hybridization platform of claim 19 wherein the second gradient is formed by varying the length of the nucleic acids or nucleic acid analogs in single base increments.

21. The hybridization platform of claim 20 wherein the second gradient spans 1,000 or more bases.

22. The hybridization platform of claim 20 wherein the second gradient spans 100 or more bases.

23. The hybridization platform of claim 20 wherein the second gradient spans 10 to about 50 bases.

24. The hybridization platform of claim 1 wherein the immobilized layer is formed as a continuous layer on the surface.

25. The hybridization platform of claim 1 wherein the immobilized layer is formed as discrete regions on the surface.

26. A biosensor for detection of one or more target molecules comprising:

a planar support; and

an immobilized layer of single stranded nucleic acids or nucleic acid analogs formed on the surface of the planar support and capable of hybridizing to the one or more target molecules;

wherein the immobilized layer is formed as either a) a continuous layer on the surface or b) as discrete regions on the surface;

the nucleic acids or nucleic acid analogs being arranged as the continuous layer, or as each region, such that the one or more parameters selected from the density, sequence, orientation or structure of the nucleic acid or nucleic acid analogs are spatially varied as a continuum in the continuous layer or in each region in one or both of a first and second dimension across the surface of the planar support so as to form at least one gradient of the one or more parameters within the continuous layer or each region; and

the one or more selected parameters includes the density of the nucleic acid or nucleic acid analogs.

27. The biosensor of claim 26 further comprising detectable labels for indicating binding of the one or more target molecules to the nucleic acids or nucleic acid analogs.

28. A kit for conducting an assay for detecting and quantifying one or more target molecules in a sample which comprises:

a planar support; and

an immobilized layer of single stranded nucleic acids or nucleic acid analogs formed on the surface of the planar support and capable of hybridizing to the one or more target molecules;

wherein the immobilized layer is formed as either a) a continuous layer on the surface or b) as discrete regions on the surface;

the nucleic acids or nucleic acid analogs being arranged as the continuous layer, or as each region, such that the one or more parameters selected from the density, sequence, orientation or structure of the nucleic acid or nucleic acid analogs are spatially varied as a continuum in the continuous layer or in each region in one or both of a first and second dimension across the surface of the planar support so as to form at least one gradient of the one or more parameters within the continuous layer or each region; and

the one or more selected parameters includes the density of the nucleic acid or nucleic acid analogs.

29. The kit of claim 28 further comprising one or more reagents to detect and quantify the one or more target molecules hybridized to the nucleic acids or nucleic acid analogs.

30. A method of forming a hybridization platform comprising:

providing a planar support, and

forming on the surface of the planar support an immobilized layer of single stranded nucleic acids or nucleic acid analogs, the immobilized layer being formed either as a) a continuous layer on the surface or b) as discrete regions on the surface, the continuous layer or each region being arranged such that one or more parameters selected from the density, sequence, orientation or structure of the nucleic acid or nucleic acid analogs are spatially varied as a continuum in the continuous layer or in each region in one or both of a first and second dimension across the surface of the planar support so as to form at least one gradient of the one or more parameters within the continuous layer or each region, wherein the one or more selected parameters includes the density of the nucleic acids or nucleic acid analogs.