Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
2006-11-14
2006-11-14
Barts, Samuel (Department: 1623)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
C536S022100, C536S023100, C536S024300, C536S025310, C536S025330, C536S025340, C435S006120
Reexamination Certificate
active
07135565
ABSTRACT:
A method of synthesizing a polynucleotide which can, for example, be used during fabrication of an array. A second nucleoside is coupled to a first nucleoside through a phosphite linkage, with the second nucleoside having a hydroxyl protecting group that is a non-carbonate protecting group. The product of the foregoing step is exposed to a composition which both oxidizes the formed phosphite to a phosphate and deprotects the protected hydroxyl of the coupled nucleoside. The method has particular application to fabricating an addressable array of polynucleotides on a substrate which carries substrate bound moieties each with a hydroxyl group.
REFERENCES:
patent: 4415732 (1983-11-01), Caruthers et al.
patent: 4458066 (1984-07-01), Caruthers et al.
patent: 4500707 (1985-02-01), Caruthers et al.
patent: 4668777 (1987-05-01), Caruthers et al.
patent: 4725677 (1988-02-01), Koster et al.
patent: 4808708 (1989-02-01), Yoshida et al.
patent: 4973679 (1990-11-01), Caruthers et al.
patent: 5132418 (1992-07-01), Caruthers et al.
patent: 34069 (1992-09-01), Koster et al.
patent: 5210264 (1993-05-01), Yau
patent: 5705621 (1998-01-01), Ravikumar
patent: 5763599 (1998-06-01), Pfleiderer et al.
patent: 5861242 (1999-01-01), Chee et al.
patent: 5874554 (1999-02-01), Gamble et al.
patent: 5908926 (1999-06-01), Pirrung et al.
patent: 6008400 (1999-12-01), Scaringe et al.
patent: 6069243 (2000-05-01), Scozzari
patent: 6147205 (2000-11-01), McGall et al.
patent: 6166198 (2000-12-01), Livingston
patent: 6207819 (2001-03-01), Manoharan et al.
patent: 6222030 (2001-04-01), Dellinger et al.
patent: 6376246 (2002-04-01), Crameri et al.
patent: 2002/0045221 (2002-04-01), Dellinger et al.
patent: 2002/0055880 (2002-05-01), Unold et al.
patent: 2003/0129589 (2003-07-01), Koster et al.
patent: 0 241 363 (1987-04-01), None
patent: 0 742 287 (1996-09-01), None
patent: 0 984 021 (1999-03-01), None
patent: 0 984 021 (1999-03-01), None
patent: 0 428 810 (1999-07-01), None
patent: 1 428 810 (1999-07-01), None
patent: WO 92/10092 (1991-11-01), None
patent: WO 96/28457 (1996-03-01), None
patent: WO98/41531 (1998-01-01), None
patent: WO 98/41531 (1998-03-01), None
patent: WO 99/54509 (1998-04-01), None
patent: WO 98/393348 (1998-05-01), None
patent: WO 00/27859 (1998-06-01), None
patent: WO 00/18778 (1999-09-01), None
patent: WO 00/61594 (2000-04-01), None
Y. Hayakawa, M. Uchiyama and R. Nyori, “Nonaqueous Oxidation of Nucleoside Phosphites to the Phosphates”, Chemical Center and Department of Chemistry, Nagoya University, Tetrahedron Letters, vol. 27, No. 35, pp. 4191-4194, 1986.
Serge L. Beaucaga and Redhakrishnam P. lyer, “Advances in the Synthesis of Oligonucleotides by the Phosphoramidite Approach”, Tetrahedron Report No. 9, vol. 48, No. 12, pp. 2223-2311, 1992; Administration, Bethesada, Maryland 20892.
Jean-Louis Fourrey and Jeanette Varenne, “Introduction of a Nonaqueous Oxidation Procedures in the Phosphite Triseter Route for Oligonucleotide Synthesis”, Tetrahedron Letters, vol. 6, No. 9, pp. 1217-1220, 1985.
European Search Report, Dec. 21, 2002, pp. 26-27.
Herald Sigmund, Thomas Maier and Wolfgang Pfleidner, “A New Type of Fluoresecene Labeling of Nucleosides, Nucleotides and Oligonucleotides”, Nucleosides & Nucleotides, 16(5&6) pp. 685-696 (1997).
Ahmad Hasan, Hong Li, Jeno Tomasz and Barbara Ramsey Shaw, “Base-boronated dinucleotides: synthesis and effect of N7-cyanoborane substitution on the base protons”, Nucleic Acids Research, 1996, vol. 24, No. 11, pp. 2150-2157.
Frank Bergman, and Wolfgang Pfleidner, The 2-Dansylethoxycarbonyl (==2-{5-(Dimethylamino) naphtixalen-1-y1}sulfonyl{ethoxycarbonyl;Dnseoc)Group for Protection of the 5′-Hydroxy Function in Oligodeoxyribonucleotide Synthesis', Helvetica Chimica Acta -vol. 77 (1994), pp. 203-214.
Michael C. Pirrung and Lora Fallon, Proofing of Photolithographic DNA Synthesis with 3′, 5′Dimethoxybenzoinyloxycarbonyl-Protected Deoxynucleoside Phosphoramidites', American Chemical Society, 1998, pp. 241-246.
Frank Bergman, Erich Kueng, Patric Iaiza, and Willi Bannwarth, “Allyl as Intemucleotide Protecting Group in DNA Synthesis to be Cleaved Off by Ammonia”, Tetrahedron, vol. 51, No. 25, pp. 6974-6976.
Mitsuo Sekine, Narihiro Masuda and Tsujiaki Hata, “Synthesis of Oligodeoxyribonucleotides Involving a Rapid Procedure for Removal of Base-Protecting Groups by Use of the 4.4′-Tris(benzoyloxy)trityl (TBTr) Group”, The Chemical Society of Japan, 59, pp. 1781-1789, Jun. 1986.
Reiko Iwase, Mitsuo Sekine, Tsujaki Hata and Kin-ichiro Miura, “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 Bond Formation”, Tetrahedron Letters, vol. 29, No. 24, pp. 2969-2972, 1988.
J. Katzhendler, S. Cohen, E. Rahamin, M. Weisz, I. Ringel and J. Deutsch, The Effect of Spacer, Linkage and Solid Support on the Synthesis of Oilgonucleotides', Tetrahedron, vol. 45, No. 9, pp. 2777-2792, 1989.
David W. Will, Gerhard Breiphol, Dietrich Langner, Jochen Knolle and Eugene Uhlmann, The Synthesis of Polyamide Nucleic Acids Using a Novel Monoethoxyrithl Protecting-Group Society', Terahedron, vol. 51, No. 44, pp. 12069-12082, 1995.
Takashi Kamimura, Masahiko Tsuchiya, Ken-ichi Urakami,Koji Koura, Mitsuo Sekine, Kazuko Shinozaki, Kin-ichiro Miura, and Tsuujiaki Hata, “Synthesis of a Dodecaribonucleotide, GUAUCAAUAAUG By Use of Fully” Protected Rinonucleotide Building Blocks', American Chemical Society, 1984, pp. 4552-4557.
Mitsuo Sekine and Tsujiaki Hata, “Synthesis of Short Oligoribonucleotides Bearing a 3′-or 5′-Terminal Phosphate by Use of 4.4′, 4″-Tris(4,5-dichlorophthalimido)trityl as a New 5′-Hydroxyl Protecting Group”, American Chemical Society, 1986, pp. 4581-4586.
Mitsuo Sekine, Narihiro Masuda and Tsujiaki Hata, “Introduction of the 4, 4′4″”-Tris(Benzoyloxy)Trityl Group into the Exo Amino Groups of Deoxyribonucleotides and its Properties', Tetrahedron, vol. 41, No. 23 pp. 5445-5453.
A. Nyilas, C. Glemarec & J. Chattopadhyaya, Synthesis of [3′(O)>5′(C)]-Oxyacetamido Linked Nucleotide Tetrahedron, vol. 46, No. 6, pp. 2149-2164, 1990.
Yoshihiro Hayakawa, “Regiodefined Synthesis and Conformational Properties of Adenyldiyl Trimers with Unsymmetrical 2′-5′and 3′ -5′Intermucleotide Linkages”, Tetrahedron, vol. 51, No. 36, pp. 9899-9916, 1995.
H. Koster, “Polymer Support Oligonucleotide Synthesis VI 1-5 Use of Inorganic Carriers”, Tetrahedron Letters, No. 16, pp. 1527-1530, 1972.
U.S. Appl. No. 09/128,052, filed Aug. 3, 1998, Douglas J. Dellinger, et al.
Michael C. Pirrung and Jean-Claude Bradley, “Comparison Methods for Photochemical Phosphoramidite -Based DNA Synthesis”, J. Org. Chem. 1995, 60 pp. 6270-6276. Department of Chemistry, P. M. Gross Chemical Laboratory, Duke University, Durnham, North Carolina 27708-0346.
Hayes Dougan, John B. HObbs, Jeffrey I. Witz and Donald m. Lyster, “Syntesis and Radiodination of a Stannyl Oligodeoxyribonucleotide”, Nucleic Acids Research, 1997, vol. 25, No. 14, pp. 2897-2901.
Shigenori Iwai and Eiko Ohtsuka, “5‘-Levulinyl and 2’-tetrahydrofuranyl protection for the synthesis of Oligoribonucleotides by the phosphoramidite approach”, Nucleic Acids Research, vol. 6, No. 20, 1988, pp. 9443-9456.
Betley Jason R.
Caruthers Marvin H.
Dellinger Douglas J.
Perbost Michael G. M.
Agilent Technologie,s Inc.
Barts Samuel
Beck Michael J.
Lewis Patrick
University of Colorado
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