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Precursors for two-step polynucleotide synthesis

Patent 7427679 Issued on September 23, 2008. Estimated Expiration Date: Icon_subject August 30, 2023. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.

Patent References

Nucleosides useful in the preparation of polynucleotides
Patent #: 4500707
Issued on: 02/19/1985
Inventor: Caruthers ,   et al.

Phosphoramidite nucleoside compounds
Patent #: 4668777
Issued on: 05/26/1987
Inventor: Caruthers ,   et al.

Solid phase synthesis of oligonucleotides using carbonate protecting groups and alpha-effect nucleophile deprotection
Patent #: 6222030
Issued on: 04/24/2001
Inventor: Dellinger, et al.

Functionalization of substrate surfaces with silane mixtures
Patent #: 6258454
Issued on: 07/10/2001
Inventor: Lefkowitz, et al.

Monomers for solid phase synthesis of oligonucleotides using carbonate protecting groups and alpha-effect nucleophile deprotection
Patent #: 6630581
Issued on: 10/07/2003
Inventor: Dellinger ,   et al.

Methods of synthesizing oligonucleotides using carbonate protecting groups and alpha-effect nucleophile deprotection
Patent #: 7101986
Issued on: 09/05/2006
Inventor: Dellinger, et al.

Exocyclic amine triaryl methyl protecting groups in two-step polynucleotide synthesis Patent #: 7193077
Issued on: 03/20/2007
Inventor: Dellinger, et al.

Inventors

Assignee

Application

No. 10652048 filed on 08/30/2003

US Classes:

536/26.7, The N-hetero ring is part of a bicyclic ring system536/26.8, The N-hereto ring is six-membered and monocyclic (e.g., uridine-5`-mono- phosphate, etc.)536/27.6, Nitrogen, other than nitro or nitroso, bonded directly to the 6-position of a purine ring system (e.g., adenosine, etc.)536/27.81, Nitrogen, other than nitro or nitroso, bonded directly to the 2-position of the purine ring system (e.g., guanosine, etc.)536/28.5Nitrogen, other than nitro or nitroso, bonded directly to the 4-position, and chalcogen bonded directly to the 2-position of the diazine ring (e.g., cytidines, etc.)

Examiners

Primary: Crane, J. E.

Foreign Patent References

  • 0241363 EP 10/01/1987
  • 1428810 EP 06/01/2004
  • WO92/10092 WO 06/01/1992

International Classes

C07H 19/10
C07H 19/20

Abstract

Precursors for use in the synthesis of polynucleotides are disclosed. The precursors include a heterocyclic base having an exocyclic amine group and a substituted or unsubstituted triaryl methyl protecting group bound to the exocyclic amine group. In particular embodiments, the precursor has the structure:

wherein: O and H represent oxygen and hydrogen, respectively, R1 is hydrido, hydroxyl, protected hydroxyl, lower alkyl, modified lower alkyl, or alkoxy, one of R2 or R3 is a hydroxyl protecting group; and the other of R2 or R3 is a reactive group capable of reacting with a reactive site hydroxyl, Base is a heterocyclic base having an exocyclic amine group, and Tram is a triaryl methyl group having the structure (V)

wherein the broken line represents a bond to the amino nitrogen of the exocyclic amine group, and R4, R5 and R6 are independently selected from unsubstituted or substituted aryl groups, provided that at least one of R4, R5, and R6 is an aryl group other than phenyl and other than substituted phenyl.

Other References

  • Iwase et al, “A New Method for the Synthesis of Capped Oligoribonucleotides by Use of an Appropriately Protected 7-Methylguanosine Diphosphate Derivative as a Donor for the Triphosphate Derivative as a Donor for the Triphosphate Bond Formation”, Tetrahedron Letters, vol. 29, No. 24, pp. 2969-2972, 1988.
  • Katzhendler et al., “The Effect of Spacer, Linkage and Solid Support on the Synthesis of Oligonucleotides”, Tetrahedron, vol. 45, No. 9, pp. 2777-2792, 1989.
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  • Sekine et al., “Synthesis of Oligodeoxyribonucleotides Involving a Rapid Procedure for Removal of Base-Protecting Groups by Use of the 4,4′, 4″- Tris(benzoyloxy) trityl (TBTr) Group”, Bull. Chem. Soc. Japan, 59, pp. 1781-1789, (1986).
  • Mishra, Rakesh K. et a., “Protecting groups as purification tool in large-scale synthesis of small oligodeoxyribonucleotides”, Indian Journal of Chemistry, 1988, 27B(9), 817-20.
  • Sekine, et al., “Synthesis of Short Oligoribonucleotides bearing a 3′—or 5′—terminal phosphates by use of 4, 4″, 4″ -tris (4, 5-dichlorophtalimido)trityl) as a new 5′ -hydroxyl protecting group” J. Amer. Chem. Society vol. 108, 1986, pp. 4581-4586.
  • Sekine, et al., “Introduction of the 4, 4′,4″-Tris (Benzoyloxy)trityl group inot the exo amino groups of into the exo amino groups of deoxyribonucleotides and its properties” Tetrahedron, vol. 41, No. 23, 1985, pp. 5445-5453.
  • Nyllas A., et al., “Synthesis of [3′(O)>5′(C)]Oxyacetamido linked nucleosides”, Tetrahedron, vol. 46, No. 6, 1990, pp. 2149-2164.
  • Brimacombe et al., “Oligonucleotidic Compounds. XXIII. Protected Derivatives of Guanosine and Adenosine 3′-Phosphate, A Synthesis of Diribonucleoside Phosphates Starting from Adenosine and Guanosine Derivatives Bearing a Free NH2 Group,” Collection Czechoslov. Chem. Commun., 33, 2074-2086 (1968).
  • Schaller et al., “Studies on Polynucleotides. XXIV. The Stepwise Synthesis of Specific Deoxyribopolynucleotides (4). Protected Derivatives of Deoxyribonucleosides and New Syntheses of Deoxyribonucleoside-3′ Phosphates,” J. Amer. Chem. Soc., 85, 3821-3827 (Dec. 5, 1963).
  • Ralph et al., “Studies on Polynucleotides. XVIII. Experiments on the Polymerization of Mononucleotides. The Synthesis and Characterization of Deoxyguanosine Oligonucleotides,”□□ J. Amer. Chem. Soc., 85, 1983-1988 (Jul. 5, 1963).
  • Smith et al., “Studies on Polynucleotides. XIV. Specific Synthesis of the C3′-C5′ Internucleotide Linkage. Synthesis of Uridylyl-(3′-5′)-Uridine and Uridylyl-(3′-5′)-Adenosine,” □□ J. Amer. Chem. Soc., 84, 430-440 (Feb. 5, 1962).
  • Michelson et al., “Nucleotides. Part III. Mononucleotides derived from Adenosine, Guanosine, Cytidine and Uridine,” Journal of the Chemical Society, 1949, pp. 2476-2486.
  • Kochetkov et al., “Reactions of Exocyclic Substituents of Nucleic Acid Bases and their Derivatives,” Chapter 6 in Organic Chemistry of Nucleic Acids, Part B, Kochetkov et al. (eds.), Plenum Press, New York, NY, 1972, only pp. 367-368 and 376-378 supplied.
  • Brimacombe et al., “Oligonucleotidic Compounds. XXIII. Protected Derivatives of Guanosine and Adenosine 3′-Phosphates. A Synthesis of Diribonucleoside Phosphates Starting from Adenosine and Guanosine Derivatives Bearing a Free NH2 Group,” Collection Czechoslov. Chem. Commun., 33, 2074-2086 (1968).
  • Schaller et al., “Studies on Polynucleotides. XXIV. The Stepwise Synthesis of Specific Deoxyribopolynucleotides (4). Protected Derivatives of Deoxyribonucleosides and New Syntheses of Deoxyribonucleoside-3′ Phosphates,” J. Amer. Chem. Soc., 85, 3821-3827 (Dec. 5, 1963).
  • Ralph et al., “Studies on Polynucleotides. XVIII. Experiments on the Polymerization of Mononucleotides. The Synthesis and Characterization of Deoxyguanosine Oligonucleotides,” J. Amer. Chem. Soc., 85, 1983-1988 (Jul. 5, 1963).
  • Smith et al., “Studies on Polynucleotides. XIV. Specific Synthesis of the C3′-C5′ Internucleotide Linkage. Synthesis of Uridylyl-(3′-5′)-Uridine and Uridylyl-(3′-5′)-Adenosine,” J. Amer. Chem. Soc., 84, 430-440 (Feb. 5, 1962).
  • Michelson et al., “Nucleotides. Part III. Mononucleotides derived from Adenosine, Guanosine, Cytidine and Uridine,” Journal of the Chemical Society, 1949, pp. 2476-2486.
  • Kochetkov et al., “Reactions of Exocyclic Substituents of Nucleic Acid Bases and their Derivatives,” Chapter 6 in Organic Chemistry of Nucleic Acids, Part B, Kochetkov et al. (eds.), Plenum Press, New York, NY, 1972, only pp. 367-368 and 376-378 supplied.
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