Method of Analyzing Nucleic Acids Using an Array of Encoded Beads

• US 20080038844A1
• Filed: 07/24/2007
• Published: 02/14/2008
• Est. Priority Date: 04/25/1996
• Status: Active Grant

• Current Assignee: BioArray Solutions Limited (Werfen SA)
• Original Assignee: BioArray Solutions Limited (Werfen SA)
• Inventors: Seul, Michael
• Granted Patent: US 8,071,393 B2
• Time in Patent Office: Days
• US Class Current: 436/526
• 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 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• 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 2219/00713 Electrochemical synthesis
• CPC Class Codes: B01L 2200/0647 Handling flowable solids, e.g. microscopic beads, cells, particles
• CPC Class Codes: B01L 2200/0652 Sorting or classification of particles or molecules
• CPC Class Codes: B01L 2200/0663 Stretching or orienting elongated molecules or particles
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0864 comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• CPC Class Codes: B01L 2300/0877 Flow chambers
• CPC Class Codes: B01L 2300/089 Virtual walls for guiding liquids
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0427 Electrowetting
• CPC Class Codes: B01L 2400/0454 radiation pressure, optical tweezers
• CPC Class Codes: B01L 3/502707 characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/50273 : characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502761 : specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C12Q 1/6825 : Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2563/155 : Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2565/501 : being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/607 : being a sensor, e.g. electrode
• CPC Class Codes: C40B 40/00 : Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: C40B 40/04 : Libraries containing only organic compounds
• CPC Class Codes: G01N 15/1468 : with spatial resolution of the texture or inner structure of the particle
• CPC Class Codes: G01N 15/149 : specially adapted for sorting particles, e.g. by their size or optical properties
• CPC Class Codes: G01N 2015/149 : Sorting the particles
• CPC Class Codes: G01N 2015/1497 : Particle shape
• CPC Class Codes: G01N 27/447 : using electrophoresis
• CPC Class Codes: G01N 33/54313 : the carrier being characterised by its particulate form
• CPC Class Codes: G01N 33/54386 : Analytical elements
• CPC Class Codes: G01N 33/6845 : Methods of identifying protein-protein interactions in protein mixtures
• CPC Class Codes: G02B 3/0012 : characterised by the manufacturing method
• CPC Class Codes: G02B 3/0056 : arranged along two different directions in a plane, e.g. honeycomb arrangement of lenses G02B3/0043 takes precedence; miniaturised objectives for electronic devices employing wafer level optics G02B13/0085
• CPC Class Codes: G02B 3/0075 : characterized by non-optical structures, e.g. having integrated holding or alignment means
• CPC Class Codes: H05H 3/04 : Acceleration by electromagnetic wave pressure
• CPC Class Codes: Y10S 435/808 : Optical sensing apparatus
• CPC Class Codes: Y10S 435/81 : Packaged device or kit
• CPC Class Codes: Y10S 435/814 : Enzyme separation or purification
• CPC Class Codes: Y10S 436/806 : Electrical property or magnetic property
• CPC Class Codes: Y10S 436/808 : Automated or kit
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays
• CPC Class Codes: Y10T 436/25125 : Digestion or removing interfering materials

Abstract

A method and apparatus for the manipulation of colloidal particulates and biomolecules at the interface between an insulating electrode such as silicon oxide and an electrolyte solution. Light-controlled electrokinetic assembly of particles near surfaces relies on the combination of three functional elements: the AC electric field-induced assembly of planar aggregates; the patterning of the electrolyte/silicon oxide/silicon interface to exert spatial control over the assembly process; and the real-time control of the assembly process via external illumination. The present invention provides a set of fundamental operations enabling interactive control over the creation and placement of planar arrays of several types of particles and biomolecules and the manipulation of array shape and size. The present invention enables sample preparation and handling for diagnostic assays and biochemical analysis in an array format, and the functional integration of these operations. In addition, the present invention provides a procedure for the creation of material surfaces with desired properties and for the fabrication of surface-mounted optical components.

Claims

1. A bioanalytical array implemented using at least one array of particles, said assay comprising:

an array of particles formed by the method of dynamically assembling the array of particles at an interface between an electrode and an electrolyte solution, the method comprising the following steps providing an electrode, an electrolyte solution and an interface therebetween;

providing a plurality of particles located in said electrolyte solution;

illuminating said electrode with a predetermined light pattern; and

generating an electric field at said interface to cause the assembly of an array of particles in accordance with the predetermined light pattern of said electrode

a biochemical protocol implementation unit which effects a biochemical interaction between said first type of molecule and a corresponding first type of analyte to form a first type of paired entity, and a biochemical interaction between said second type of molecule and a corresponding second type of analyte to form a second type of paired entity.

2. The assay of claim 1, further comprising:

a detector for detecting the existence of one of said paired entities;

a decoder for determining the different types of particles; and

a correlator which operates on the output of the detector and the decoder to indicate which types of particles include paired entities.

3. A method of implementing a bioanalytical assay comprising the following steps:

dynamically assembling an array of particles at an interface between an electrode and an electrolyte solution, the method comprising the following steps;

providing an electrode, an electrolyte solution and an interface therebetween;

providing a plurality of particles located in said electrolyte solution, said plurality of particles including a first type of particle and a second type of particle different from said first type;

illuminating said electrode with a predetermined light pattern; and

generating an electric field at said interface to cause the assembly of an array of particles in accordance with the predetermined light pattern of said electrode; and

implementing a biochemical protocol which effects a biochemical interaction between said first type of molecule and a corresponding first type of analyte to form, a first type of paired entity, and a biochemical interaction between said second type of molecule and a corresponding second type of analyte to form a second type of paired entity.

4. The method of claim 3, further comprising the following steps:

detecting the existence of one of said paired entities;

determining the different types of particles; and

correlating the output of the detector and the decoder to indicate which types of particles include paired entities.

5. The method of claim 3, further comprising the step of marking individual distinguishable particles within said particle array by initiating a photochemical color-reaction in response to targeting said particles with a focused illumination source.

6. The method of claim 3, further comprising the step of re-configuring said particle using interactive adjustments of said predetermined illumination pattern to isolate distinguishable particles within said array.

7. The method of claim 3, further comprising the following steps:

attaching a plurality of types of molecules to the surface of said particles, each said particle having a plurality of molecules or one type;

attaching a single distinct type of molecule to said electrode surface;

introducing a plurality of said particles having a plurality of types of molecules into said electrolyte solution; and

disassembling said particle array, retaining and thereby selecting from the plurality of types of molecules initially introduced only those particles having specific types of molecules of demonstrated biochemical affinity for molecules on said electrode surface.

8. The method of claim 7, wherein said particles include antibody-producing cells.

9. The method of claim 3, further comprising the following steps:

attaching a plurality of types of molecules to the surface of said particles, each said particle having a plurality of molecules of one type;

attaching a single distinct type of biological target to said electrode surface;

releasing molecules from said particles at a predetermined location by separating said molecules from said particles in response to a chemical or photochemical stimulus under conditions favoring the biochemical interaction and formation of paired entities between molecules released from said particles and biological targets displayed on said electrode surface; and

marking for identification such types of said particles having molecules which when released cause a detectable response in proximal biological targets.

10. The method of claim 9, wherein said biological targets include cells grown in culture on said electrode, said cells being modified in a detectable way by exposure to said first type of molecules released from said particle array.

11. The method of claim 3, wherein said paired entities include at least one of receptor-ligand, antibody-antigen and enzyme-substrate.

12. The method of claim 3, wherein said paired entities include matching strands of oligonucleotides or strands of DNA or RNA, and formation of said paired entities involves hybridization.

13. A method for performing multiple chemical and biochemical analytical procedures using at least one particle array, said method comprising the following steps:

providing an electrode and an electrolyte solution having an interface therebetween;

generating an electric field at an interface between an electrode and an electrolyte solution;

patterning said electrode to modify the electrochemical properties of said electrode;

illuminating said surface with a predetermined light pattern to control the movement of said particles in accordance with said predetermined light pattern and the electrochemical properties of said electrode;

performing a first procedure on a portion of said particles to produce a first reaction set of particles;

isolating said first reaction set of particles in accordance with said predetermined light pattern; and

performing a second procedure on said first reaction set of particles to produce a second reaction set of particles.

14. The method of claim 13, wherein said performing and isolating steps are interactively controlled in real time by way of an adjustable illumination pattern.

15. The method of claim 13, wherein said performing and isolating steps are dynamically reconfigurable.

16. A method of manipulating nucleic acid, including DNA or RNA, comprising the following steps:

providing an electrode, an electrolyte solution and an interface therebetween;

providing a plurality of nucleic acid molecules in said electrolyte solution, said nucleic acid molecules being in a coiled configuration;

generating an electric field at said interface to cause the movement of said particles;

illuminating said electrode with a predetermined light pattern to create controlled gradients in the flow velocity across the nucleic acid, said velocity gradient causing different portions of the nucleic acid to move at different velocities such that the nucleic acid is stretched in the direction of the local velocity gradient; and

maintaining a stagnation point of zero velocity such that the nucleic acid is substantially fixed in position.

17. A bioanalytical assay implemented using at least one array of particles, said particles being suspended at an interface between an electrode and an electrolyte solution, said assay comprising:

an electrode and an electrolyte solution therebetween;

a plurality of molecules located in said electrolyte, said molecules including a first type of molecule and a second type of molecule;

a biochemical protocol implementation unit which effects a biochemical interaction between said first and second types of molecules, said interaction resulting in the formation of paired entities, and said implementation unit operating to detect the formation of said paired entity;

a plurality of particles located in said electrolyte solution;

an electric field generator which generates an electric field at said interface;

said electrode being patterned to include at least one area of modified electrochemical properties; and

an illumination source positioned to illuminate said surface with a predetermined light pattern to control the movement of said particles in accordance with said predetermined light pattern and the electrochemical properties of said electrode.

18. An apparatus for performing multiple chemical and biochemical analytical procedures using at least one particle array, said apparatus comprising:

an electrode and an electrolyte solution having an interface therebetween;

an electric field generator which generates an electric field at an interface between an electrode and an electrolyte solution;

said electrode being patterned to modify the electrochemical properties of said electrode;

an illuminating source which illuminates said surface with a predetermined light pattern to control the movement of said particles in accordance with said predetermined light pattern and the electrochemical properties of said electrode;

means for performing a first procedure on a portion of said particles to produce a first reaction set of particles;

means for isolating said first reaction set of particles in accordance with said predetermined light pattern; and

means for performing a second procedure on said first reaction set of particles to produce a second reaction set of particles.

19. An apparatus for manipulating nucleic acid, including DNA or RNA, said apparatus comprising:

an electrode, an electrolyte solution and an interface therebetween;

a plurality of nucleic acid molecules in said electrolyte solution, said nucleic acid molecules being in a coiled configuration;

an electric field generator which generates an electric field at said interface to cause the movement of said particles;

said electrode being patterned to include areas of modified electrochemical properties which in conjunction with said electric field create controlled gradients in the flow velocity across the nucleic acid, said velocity gradient causing different portions of the nucleic acid to move at different velocities such that the nucleic acid is stretched in the direction of the local velocity gradient, wherein a stagnation point of zero velocity is maintained such that the nucleic acid is substantially fixed in position; and

an illumination source which illuminates said electrode with a predetermined light pattern to create controlled gradients in the flow velocity across the nucleic acid, said velocity gradient causing different portions of the nucleic acid to move at different velocities such that the nucleic acid is stretched in the direction of the local velocity gradient.