Apparatus for forming polynucleotides or polypeptides

• US 6,420,169 B1
• Filed: 11/30/1994
• Issued: 07/16/2002
• Est. Priority Date: 06/07/1989
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Fodor, Stephen P.A., Pirrung, Michael C., Stryer, Lubert, Read, J. Leighton, Hoeprich, Paul D. Jr.
• Primary Examiner(s): Ponnaluri, Padmashri
• Application Number:
  US08/348,471
• Time in Patent Office: 2,785 Days
• Field of Search: 435/6, 435/969, 435/289.1, 435/292.1, 435/DIG.43, 435/DIG.44, 536/25.3, 436/518, 436/527, 436/807, 530/335, 422/131, 935/88
• US Class Current: 435/289.1
• 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 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00434 Liquid crystal masks
• CPC Class Codes: B01J 2219/00436 Maskless processes
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00475 Sheets
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• 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 2219/00608 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 2219/00648 : by the use of solid beads
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01L 7/52 : with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• 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 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07C 229/14 : to carbon atoms of carbon skeletons containing rings
• CPC Class Codes: C07C 229/16 : to carbon atoms of hydrocarbon radicals substituted by amino or carboxyl groups, e.g. ethylenediamine-tetra-acetic acid, iminodiacetic acids
• CPC Class Codes: C07D 263/44 : Two oxygen atoms
• CPC Class Codes: C07D 317/62 : with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to atoms of the carbocyclic ring
• CPC Class Codes: C07H 19/04 : Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• CPC Class Codes: C07H 19/10 : with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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 1/042 : characterised by the nature of the carrier
• 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: C07K 17/06 : attached to the carrier via a bridging agent
• CPC Class Codes: C07K 17/14 : Peptides being immobilised on, or in, an inorganic carrier
• CPC Class Codes: C07K 7/06 : having 5 to 11 amino acids
• CPC Class Codes: C12Q 1/6809 : Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• 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 60/14 : for creating libraries
• CPC Class Codes: G01N 15/1433 : using image recognition
• 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: G03F 7/00 : Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printing surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor using photoresist structures for special production processes, see the relevant places, e.g. B44C, H01L, e.g. H01L21/00, H05K
• CPC Class Codes: G03F 7/26 : Processing photosensitive materials; Apparatus therefor G03F7/12 - G03F7/24 take precedence
• CPC Class Codes: G03F 7/265 : Selective reaction with inorganic or organometallic reagents after image-wise exposure, e.g. silylation
• CPC Class Codes: G03F 7/38 : Treatment before imagewise removal, e.g. prebaking G03F7/265 takes precedence
• 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: Y02P 20/55 : Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
• CPC Class Codes: Y10S 436/809 : Multifield plates or multicontainer arrays

Abstract

A method for synthesizing oligonucleotides on a solid substrate. The method provides for the irradiation of a first predefined region of the substrate without irradiation of a second predefined region of the substrate. The irradiation step removes a protecting group therefrom. The substrate is contacted with a first nucleotide to couple the nucleotide to the substrate in the first predefined region. By repeating these steps, an array of diverse oligonucleotides is formed on the substrate.

Claims

1. An apparatus for forming polynucleotides, said apparatus comprising:

a body having a cavity therein, said cavity being less than 1000 μ

m deep;

a substrate comprising a surface mated to said body, whereby said surface contacts and seals said cavity, wherein said surface has functional groups in fluid communication with said cavity and reactive with nucleosides or nucleotides, and

an inlet port and an outlet port, said inlet port and said outlet port being in fluid communication with said cavity.

5. The apparatus as recited in claim 1 wherein the functional groups are protected with MeNPOC.

2. An apparatus for forming polynucleotides, said apparatus comprising:

a body having a sealed cavity disposed therein, said cavity being less than 1000 μ

m deep and comprising a substrate having a surface, wherein said surface has functional groups reactive with nucleotides or nucleosides; and

an inlet port and an outlet port, said inlet port and said outlet port being in fluid communication with said cavity; and

a means for providing ultrasonic radiation in said cavity.

3. An apparatus for forming polynucleotides, said apparatus comprising:

a body having a sealed cavity disposed therein, said cavity being less than 500 μ

m deep;

a substrate comprising a surface mated to said body, whereby said surface contacts and seals said cavity, wherein said surface has functional groups in fluid communication with said cavity and reactive with nucleotides or nucleosides; and

an inlet port and an outlet port, said inlet port and said outlet port being in fluid communication with said cavity.

4. The apparatus as recited in claim 3 wherein said functional groups are protected with a protective group.

6. The apparatus of claim 4, wherein the protective group is nitroveratryloxycarbonyl.

7. An apparatus for forming polynucleotides, said apparatus comprising:

a glass substrate having a surface comprising linker molecules bearing functional groups reactive with nucleotides or nucleosides, said surface mated to a body having a cavity for sealing said cavity such that said linker molecules are in fluid communication with said cavity wherein said cavity is being less than 1000 μ

m deep;

an inlet port and an outlet port, said inlet port and said outlet port being in communication with said cavity, wherein said cavity is less than 1000 μ

m deep;

a fluid flowing means coupled to said inlet port.

8. An apparatus for forming polypeptides, said apparatus comprising:

a body having a sealed cavity disposed therein, said cavity being less than 1000 μ

m deep;

a substrate comprising a surface mated to said body, whereby said surface contacts and seals said cavity, wherein said surface has functional groups in fluid communication with said cavity and reactive with amino acids; and

an inlet port and an outlet port, said inlet port and said outlet port being in fluid communication with said cavity.

9. The apparatus of claim 8, further comprising a pump positioned to flow said fluid into said cavity through said inlet port and out of said cavity through said outlet port.

10. An apparatus for forming polypeptides, said apparatus comprising:

a body having a sealed cavity disposed therein, said cavity being less than 1000 μ

m deep and comprising a substrate having a surface, wherein said surface has functional groups reactive with amino acids; and

an inlet port and an outlet port, said inlet port and said outlet port being in fluid communication with said cavity; and

a means for providing ultrasonic radiation in said cavity.

11. An apparatus for forming polypeptides, said apparatus comprising:

a body having a sealed cavity disposed therein, said cavity being less than 500 μ

m deep;

a substrate comprising a surface mated to said body, whereby said surface contacts and seals said cavity, wherein said surface has functional groups in fluid communication with said cavity and reactive with amino acids; and

an inlet port and an outlet port, said inlet port and said outlet port being in fluid communication with said cavity.

12. The apparatus as recited in claim 11 wherein said functional groups are protected with a protective group.

13. The apparatus as recited in claim 12 wherein said protective group comprises MeNPOC.

14. The apparatus of claim 12, wherein the protective group is nitroveratryloxycarbonyl.

15. An apparatus for forming polypeptides, said apparatus comprising:

a glass substrate having a surface comprising linker molecules with functional groups reactive with amino acids, said surface mated to a body having a cavity for sealing said cavity such that said linker molecules are in fluid communication with said cavity;

wherein said cavity is being less than 1000 μ

m deep;

an inlet port and an outlet port, said inlet port and said outlet port being in communication with said cavity, wherein said cavity is less than 1000 μ

m deep;

a fluid flowing means coupled to said inlet port positioned to deliver fluid to the cavity and

a means for heating said cavity.