Method for the electronic analysis of a sample oligonucleotide sequence

• US 8,389,212 B1
• Filed: 07/22/1999
• Issued: 03/05/2013
• Est. Priority Date: 11/01/1993
• Status: Expired due to Fees

• Current Assignee: Gamida for Life B.V.
• Original Assignee: Gamida for Life B.V.
• Inventors: Heller, Michael J., Tu, Eugene
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US09/358,788
• Time in Patent Office: 4,975 Days
• Field of Search: 435/6, 536/25.3, 422/50, 422/68.1, 436/501
• US Class Current: 435/6.1
• 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 19/0093 Microreactors, e.g. miniaturised or microfabricated reactors laboratory containers with capillary fluid transport in microfabricated channels or chambers B01L3/5027
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00527 Sheets
• 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 2219/00605 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 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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 2219/00686 Automatic
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00713 : Electrochemical 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: B01L 2300/0636 : Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0645 : Electrodes
• CPC Class Codes: B01L 2300/0829 : Multi-well plates; Microtitration plates
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2400/0421 : electrophoretic flow
• 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 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 10/00 : Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 5/00 : Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07K 1/04 : on carriers C07K1/003, C07K1/006 take precedence
• CPC Class Codes: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C12Q 1/6813 : Hybridisation assays
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• 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 2565/515 : characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C12Q 2565/607 : being a sensor, e.g. electrode
• 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 60/14 : for creating libraries
• CPC Class Codes: G01N 27/3276 : being a hybridisation with immobilised receptors using a FET type sensor G01N27/4145; concerning the hybridisation C12Q1/68
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules
• CPC Class Codes: G11C 19/00 : Digital stores in which the information is moved stepwise, e.g. shift registers
• CPC Class Codes: H01L 2224/45124 : Aluminium (Al) as principal constituent
• CPC Class Codes: H01L 2224/45144 : Gold (Au) as principal constituent
• CPC Class Codes: H01L 2224/48 : of an individual wire connector
• CPC Class Codes: H01L 2224/95085 : being a liquid, e.g. for fluidic self-assembly
• CPC Class Codes: H01L 2224/95145 : Electrostatic alignment, i.e. polarity alignment with Coulomb charges
• CPC Class Codes: H01L 24/95 : at chip-level, i.e. with connecting carried out on a plurality of singulated devices, i.e. on diced chips
• CPC Class Codes: H01L 25/50 : Multistep manufacturing processes of assemblies consisting of devices, each device being of a type provided for in group H01L27/00 or H01L29/00 H01L21/50 takes precedence
• CPC Class Codes: H01L 29/6656 : using multiple spacer layers, e.g. multiple sidewall spacers
• CPC Class Codes: H01L 29/6659 : with both lightly doped source and drain extensions and source and drain self-aligned to the sides of the gate, e.g. lightly doped drain [LDD] MOSFET, double diffused drain [DDD] MOSFET
• CPC Class Codes: H01L 29/66628 : recessing the gate by forming single crystalline semiconductor material at the source or drain location
• CPC Class Codes: H01L 29/7834 : with a non-planar structure, e.g. the gate or the source or the drain being non-planar
• CPC Class Codes: H01L 2924/00 : Indexing scheme for arrangements or methods for connecting or disconnecting semiconductor or solid-state bodies as covered by H01L24/00
• CPC Class Codes: H01L 2924/00014 : the subject-matter covered by the group, the symbol of which is combined with the symbol of this group, being disclosed without further technical details
• CPC Class Codes: H01L 2924/09701 : Low temperature co-fired ceramic [LTCC]
• CPC Class Codes: H01L 2924/10253 : Silicon [Si]
• CPC Class Codes: H01L 2924/12033 : Gunn diode
• CPC Class Codes: H01L 2924/12043 : Photo diode
• CPC Class Codes: H01L 2924/15788 : Glasses, e.g. amorphous oxides, nitrides or fluorides
• CPC Class Codes: Y10S 435/808 : Optical sensing apparatus
• CPC Class Codes: Y10S 435/814 : Enzyme separation or purification
• CPC Class Codes: Y10S 436/805 : Optical property
• CPC Class Codes: Y10T 436/25125 : Digestion or removing interfering materials

Abstract

A self-addressable, self-assembling microelectronic device is designed and fabricated to actively carry out and control multi-step and multiplex molecular biological reactions in microscopic formats. These reactions include nucleic acid hybridization, antibody/antigen reaction, diagnostics, and biopolymer synthesis. The device can be fabricated using both microlithographic and micro-machining techniques. The device can electronically control the transport and attachment of specific binding entities to specific micro-locations. The specific binding entities include molecular biological molecules such as nucleic acids and polypeptides. The device can subsequently control the transport and reaction of analytes or reactants at the addressed specific micro-locations. The device is able to concentrate analytes and reactants, remove non-specifically bound molecules, provide stringency control for DNA hybridization reactions, and improve the detection of analytes. The device can be electronically replicated.

Claims

1. A method for analyzing a sample oligonucleotide sequence in solution comprising:

(a) forming a plurality of individually electronically addressable microscopic locations on a substrate, each microscopic location comprising a micro-electrode;

(b) providing a permeation layer adjacent to said micro-electrode in each of said microscopic locations, said permeation layer having selective diffusion properties thereby permitting the free transport of counter-ions to said micro-electrode and inhibiting large binding entities from physical contact with said micro-electrode;

(c) providing an attachment layer adjacent to said permeation layer in each of said microscopic locations;

(d) electronically immobilizing one or more anchor sequences to said attachment layer in individually selected microscopic locations, wherein said one or more anchor sequences comprise oligonucleotide sequences capable of hybridizing with said sample oligonucleotide sequence;

(e) contacting said sample oligonucleotide sequence with said one or more anchor sequences thereby allowing said sample oligonucleotide sequence to hybridize to said one or more anchor;

(f) subjecting said individually selected microlocations to a continuous and constant electric field which moves unhybridized and partially hybridized sample oligonucleotide sequences away from said one or more anchor;

(g) determining whether said sample oligonucleotide sequence is hybridized to said one or more anchor sequences; and

controlling a level of stringency of hybridization, by adjusting a power level of said electric field and/or a length of time said individually selected microlocations are subjected to said electric field in step (f), to improve said analyzing of the sample oligonucleotide sequence, by enabling ensuring removal of partially hybridized sequences and improving the resolution of single mis-match hybridizations.

2. The method of claim 1, wherein step (e) additionally comprises subjecting said individually selected microlocations to an electric field which concentrates said sample oligonucleotide sequence near said one or more anchor sequences.

3. The method of claim 1, wherein each one of said one or more anchor sequences is from 6 to 100 bases.

4. The method of claim 1, wherein said sample oligonucleotide sequence is free to move and be transported between said microscopic locations on said substrate.

5. The method of claim 1, wherein step (g) further comprises:

(i) adding a probe comprising an oligonucleotide sequence capable of hybridizing to a target oligonucleotide sequence forming part of said sample oligonucleotide sequence that is not hybridized to said one or more anchor sequences, thereby allowing said probe to hybridize to said target oligonucleotide sequence;

(ii) subjecting said individually selected microscopic locations to an electric field which moves unhybridized probe oligonucleotide sequences away from said one or more anchor sequences; and

(iii) determining whether said probe is hybridized to said target oligonucleotide sequence.

6. The method of claim 1, wherein said permeation layer, said attachment layer, or both, are made from aminopropyltriethoxy silane.

7. A method for analyzing a sample oligonucleotide sequence in solution comprising:

(a) forming a plurality of individually electronically addressable microscopic locations on a substrate, each microscopic location comprising a micro-electrode, and said sample oligonucleotide sequence is free to move and be transported between said microscopic locations on said substrate;

(b) providing a permeation layer adjacent to said micro-electrode in each of said microscopic locations, said permeation layer having selective diffusion properties thereby permitting the free transport of counter-ions to said micro-electrode and inhibiting large binding entities from physical contact with said micro-electrode;

(c) providing an attachment layer adjacent to said permeation layer in each of said microscopic locations;

(d) electronically immobilizing one or more anchor sequences to said attachment layer in individually selected microscopic locations, wherein said one or more anchor sequences comprise oligonucleotide sequences capable of hybridizing with said sample oligonucleotide sequence;

(e) contacting said sample oligonucleotide sequence with said one or more anchor sequences thereby allowing said sample oligonucleotide sequence to hybridize to said one or more anchor;

(f) subjecting said individually selected microlocations to a continuous and constant electric field which moves unhybridized and partially hybridized sample oligonucleotide sequences away from said one or more anchor;

(g) determining whether said sample oligonucleotide sequence is hybridized to said one or more anchor sequences; and

controlling a level of stringency of hybridization, by adjusting a power level of said electric field and/or a length of time said individually selected microlocations are subjected to said electric field in step (f), to improve said analyzing of the sample oligonucleotide sequence, by enabling ensuring removal of partially hybridized sequences and improving the resolution of single mis-match hybridizations.