Nucleotides and analogs having photoremoveable protecting groups

• US 6,310,189 B1
• Filed: 01/25/2000
• Issued: 10/30/2001
• 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: Pirrung, Michael C., Fodor, Stephen P. A., Stryer, Lubert, Read, J. Leighton
• Primary Examiner(s): Zitomer, Stephanie
• Assistant Examiner(s): FORMAN, BETTY J
• Application Number:
  US09/490,580
• Time in Patent Office: 644 Days
• Field of Search: 536/25.3, 536/23.1, 536/24.3, 536/24.33, 536/25.31, 435/91.1, 435/89
• US Class Current: 536/22.1
• 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 2219/00612 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 2219/00648 : 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: 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 21/253 : for batch operation, i.e. multisample apparatus analytical automats G01N35/00
• 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 7/265 : 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

Abstract

A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protective groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.

Claims

1. A compound having a photoremoveable protecting group covalently attached to a C-3′

or C-5′

oxygen atom, wherein said compound is selected from the group consisting of natural or unnatural nucleoside phosphoramidites and natural or unnatural nucleoside H-phosphonates.

2. A compound of claim 1, wherein said oxygen atom is a C-5′

oxygen of a ribonucleoside phosphoramidite or a ribonucleoside H-phosphonate.

3. A compound of claim 1, wherein said oxygen atom is a C-5′

oxygen of a deoxyribonucleoside phosphoramidite or a deoxyribonucleoside H-phosphonate.

4. A compound of claim 1, wherein said oxygen atom is a C-5′

oxygen of a natural nucleoside phosphoramidite.

5. A compound of claim 1, having the formula:

wherein

B is selected from the group consisting of natural or unnatural adenine, natural or unnatural guanine, natural or unnatural thymine, natural or unnatural cytosine, and natural or unnatural uracil;

R is selected from the group consisting of hydrogen, hydroxy, protected hydroxy, halogen and alkoxy;

P is a phosphoramidite or H-phosphonate group; and

PG is a photoremoveable protected group.

6. A compound of claim 5, wherein R is hydrogen or hydroxy.

7. A compound of claim 5, wherein P is a 2-cyanoethylphosphoramidite group.

8. A compound of claim 5, wherein B is selected from the group consisting of adenine, thymine, uracil, cytosine and guanine.

9. A compound of claim 5, wherein PG is a photoremoveable protecting group having a nitrophenyl moiety.

10. A compound of claim 5, wherein PG is a photoremoveable protecting group selected from the group consisting of NVOC, MeNPOC, NPOC and MeNVOC.

11. A compound of claim 5, wherein B is selected from the group consisting of adenine, thymine, uracil, cytosine and guanine, R is hydrogen or hydroxy, P is a 2-cyanoethylphosphoramidite group, and PG is a photoremoveable protecting group selected from the group consisting of NVOC, MeNPOC, MeNVOC and NPOC.

12. A method for preparing a compound of claim 1, said method comprising attaching a photoremoveable protecting group to a C-3′

or C-5′

oxygen atom of a compound selected from the group consisting of natural or unnatural nucleoside phosphoramidites and natural or unnatural nucleoside H-phosphonates.

13. A method of claim 12, wherein said compound is selected from the group consisting of natural nucleoside phosphoramidites and natural nucleoside H-phosphonates.

14. A method of claim 12, wherein said compound is selected from the group consisting of natural deoxyribonucleoside phosphoramidites.

15. A method of claim 12, wherein said photoremoveable protecting group is attached to the C5′

hydroxy group of a compound having the formula;

wherein

B is selected from the group consisting of natural or unnatural adenine, natural or unnatural guanine, natural or unnatural thymine, natural or unnatural cytosine, and natural or unnatural uracil;

R is selected from the group consisting of hydrogen, hydroxy, protected hydroxy, halogen and alkoxy; and

P is a phosphoramidite or H-phosphonate group.

16. A method of claim 15, wherein B is selected from the group consisting of adenine, guanine, cytosine, uracil and thymine and R is hydrogen or hydroxy.

17. A method of activating a terminal nucleotide in a nucleic acid, said terminal nucleotide having a photoremoveable protecting group, said method comprising removing said photoremoveable protecting group from a latent C5′

hydroxy moiety in said nucleic acid.