Spatially-addressable immobilization of oligonucleotides and other biological polymers on surfaces

• US 5,412,087 A
• Filed: 04/24/1992
• Issued: 05/02/1995
• Est. Priority Date: 04/24/1992
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymax Incorporated
• Inventors: McGall, Glenn H., Fodor, Stephen P. A., Sheldon, Edward L.
• Primary Examiner(s): Robinson, Douglas W.
• Assistant Examiner(s): VARMA, ANITA NMN
• Application Number:
  US07/874,849
• Time in Patent Office: 1,103 Days
• Field of Search: 436/527, 436/528, 436/578, 436/507, 436/807, 436/961, 436/962, 436/973, 435/187, 536/27, 536/24.3, 536/22.1
• US Class Current: 536/24.3
• 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 2219/00364 Pipettes
• CPC Class Codes: B01J 2219/00367 capillary
• CPC Class Codes: B01J 2219/00369 in multiple or parallel arrangements
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00389 Feeding through valves
• CPC Class Codes: B01J 2219/00416 Vacuum
• CPC Class Codes: B01J 2219/0043 for direct application of reagents, e.g. through openings in a shutter
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• 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 2219/00536 in the shape of disks
• 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 2219/00626 : Covalent
• CPC Class Codes: B01J 2219/0063 : Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00686 : Automatic
• 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: 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: 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 1/045 : 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: 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: Y02P 20/55 : Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
• CPC Class Codes: Y10S 530/816 : Attached to the carrier via a bridging agent

Abstract

Substrates with surfaces comprising compounds with thiol functional groups protected with a photoremovable protecting group can be used to construct arrays of immobilized anti-ligands, such as oligonucleotide probes or other biological polymers. The arrays can be used in assays to detect the presence of complementary nucleic acids in a sample. Spatially addressed irradiation of predefined regions on the surface permits immobilization of oligonucleotides and other biological polymers at the activated regions on the surface. Cycles of irradiation on different regions of the surface and immobilization of different anti-ligands allow formation of an immobilized matrix of anti-ligands at defined sites on the surface. The immobilized matrix of anti-ligands permits simultaneous screenings of a liquid sample for ligands having high affinities for certain anti-ligands of the matrix.

Claims

1. A method for forming predefined regions on a surface of a solid support, the method comprising the steps of:

a) covalently coupling thiolpropionate having a photochemically removable protecting group, the protecting group selected from the group consisting of nitroveratryl, 1-pyrenylmethyl, 6-nitroveratryloxycarbonyl, dimethyldimethoxybenzyloxycarbonyl, nitrobenzyloxycarbonyl, 5-bromo-7-nitroindolinyl, O-hydroxy-alpha-methyl-cinnamoyl, methyl, 6-nitroveratryloxycarbonyl, methyl-6-nitropiperonyloxycarbonyl, and 2-oxymethylene anthraquinone, to functional groups on a surface of a solid support; and

b) illuminating the surface with a light source of a wavelength of between 280 and 420 nm shone through a mask, thereby selectively irradiating the predefined regions of the surface to remove said photochemically removable protecting group from the thiolpropionate in the predefined regions.

2. The method of claim 1, wherein the solid support is a functionalized glass slide and the photochemically removable protecting group is nitroveratryl.

3. The method of claim 2, wherein said functionalized glass slide has been functionalized by treatment with t-BOC-aminopropyltriethoxysilane.

4. The method of claim 2, wherein the method further comprises covalently coupling and activated oligonucleotide to the deprotected thiolpropionate in said predefined regions.

5. The method of claim 4, wherein said activated oligonucleotide has been activated with succinimidyl 6-maleimidylhexanoate.

6. The method of claim 3, wherein the coupling step is carried out in the presence of a cationic detergent.

7. The method of claim 6, wherein the cationic detergent is dodecyl trimethyl ammonium bromide (DTAB).