Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives
Reexamination Certificate
2007-02-27
2007-02-27
Qian, Celine (Department: 1636)
Organic compounds -- part of the class 532-570 series
Organic compounds
Carbohydrates or derivatives
Reexamination Certificate
active
09894423
ABSTRACT:
A novel method for the labeling of oligonucleotides which results in the economical synthesis of 5′ labeled molecules. A set of suitably protected and carefully selected set of amino linkers, a modified deprotination/cleavage protocol and standard coupling methodologies to are used to allow for the convergent synthesis of any number of labeled oligonucleotides.
REFERENCES:
patent: 4415732 (1983-11-01), Caruthers et al.
patent: 4500707 (1985-02-01), Caruthers et al.
patent: 4668777 (1987-05-01), Caruthers et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis et al.
patent: 4762779 (1988-08-01), Snitman
patent: 4973679 (1990-11-01), Caruthers et al.
patent: 5218103 (1993-06-01), Caruthers et al.
patent: 5231191 (1993-07-01), Woo et al.
patent: 5278302 (1994-01-01), Caruthers et al.
patent: 5453496 (1995-09-01), Caruthers et al.
patent: 6255476 (2001-07-01), Vinayak et al.
Caruthers et al., “Chemical Synthesis of Deoxyoligonucleotides by the Phosphoramidite Method,”Methods in Enzymology154:287-313 (1987).
Doty et al., “Strand Separation and Specific Recombination in Deoxyribonucleic Acids: Physical Chemicals Studies,”Proc. Natl. Acad. Sci.USA 46:461 (1960).
Horvath et al., “An Automated DNA Synthesizer Employing Deoxynucleoside 3′-Phosphoramidites,”Methods in Enzymology154:314-326 (1987).
Hung et al., “Energy Transfer Primers with 5- or 6-Carboxyrhodamine-6G as Acceptor Chromophores,”Analytical Biochem., 238, 165-170, (1996).
Igloi, “Stratedies for introducing non-radioactive labels during the automated sequence analysis of necleic acids,”ELB Electronic Journal of Biotechnology1(1):1-8 (1998).
Jang et al., “Ligation mediated fluorescent labeling of DNA sequencing primers,”Nucleic Acids Research25(4):922-923 (1997).
Joslin Diabetes Center, DNA Core Facility, “DNA Stnthesis Steps,” Revised Sep. 10, 1999 dnacore.joslab.harvard.edu/core/cycle.html.
Lyttle et al., “Versatile Linker Chemistry for Synthesis of 3′-Modified DNA,”Bioconjugate Chem8:193-198 (1997).
Marmur and Lane, “Strand Separation and Specific Recombination in Deoxyribonucleic Acids: Biological Studies,”Proc. Natl. Acad. Sci. USA 46:453-461 (1960).
Paladichuk, “Fishing in a Molecular Sea,”The Scientist13(2):19 (1999), www.the-scientist.com/yr1999/jan/profile1—990118.html.
Pon, “Tips for Oligonucleotide Synthesis,” www.abrf.org/ABRFNews/1994/December1994/dec94ponoligo.html.
Rios, “Phosphoramidite Chemistry,” sonhouse.hunter.cuny.edu/facilities/sequence/phoschem.htlm.
Sinha et al., “The preparation and application of functionalised synthetic oligonucleotides: III. Use of H-phosphonate derivatives of protected amino-hexanol and mercapto-propanol or-hexanol,”Nucleic Acids Research16(6):2659-2669 (1988).
Wilkinson, “Oligo Factory, A Profile of Automated Nucleic Acid Synthesizers,”The Scientist13(21):18 (1999) www.the-scientist.com/yr1999/oct/profile1—991025.html.
T. Maniatis et al.,Molecular Cloning, Cold Spring Harbor Laboratory, 188-190 (1982).
R. J. Slater, “The Extraction and Fractionation of RNA,”In: Techniques in Molecular Biology, J.M. Walker and W. Gaastra, eds., Macmillan, NY15, 113-120 (1983).
P. Chomczynski and N. Sacchi, “Single-step Method of RNA Isolation by Acid Guanidnium Thiocyanate-Phenol-Chloroform Extraction,”Anal. Biochem. 162:156-159 (1987).
R.H. Alul et al., “Oxaly-CPG: A Labile Support For Synthesis of Sensitive Oligonucleotide Derivatives,”Nucleic Acids Res., 19(7):1527 (1991).
K.-P. Stengele and W. Pfleiderer, “Improved Synthesis of Oligodeoxyribonucleotides,”Tetrahed. Lett., 31(18):2549-2552 (1990).
B.S. Sproat and D.M. Brown, “A New Linkage For Solid Phase Synthesis of Oligodeoxyribonucleotides,”Nucleic Acids Res. 13:8, 2979-2987 (1985).
Wallace et al., “Application of Synthetic Oligonucleotides to the Diagnosis of Human Genetic Diseases,”Biochimie67:755-762 (1985).
Studencki and Wallace, “Allele-Specific Hybridization Using Oligonucleotide Probes of Very High Specific Activity: Discrimination of the Human βU- and βs-Globin Genes,”DNA3(1): 7-15 (1984).
Studencki et al., “Discrimination Among the Human βA, βB, and βC-Globin Genes Using Allele-Specific Oligonucleotide Hybridization Probes,”American Journal of Human Genetics37:42-51 (1985).
Guide to Molecular Cloning Techniques, Ed. S.L. Berger and A.R. Kimmel,Methods in Enzymology152:401 (1987).
G. Alvarado-Urbina et al., “Automated Synthesis of Gene Fragments,”Science214:270-274 (1981).
Operating Manual, “cDNA Synthesis and Cloning,” Pharmacia Biotech (1994).
Catalog, “Nucleic Acid: purification, detection and labeling,” Promega Corporation.
Catalog, “Oligotex-dT mRNA Kits,” Qiagen Corporation.
Hansen and Braman, “Isolation of Pure RNA from Micro Amounts of Tissue or Cells in 30 Minutes,”Stratagen Cloning Systems, 6:50.
Catalog, “Nucleic Acid Isolation and Purification,” U.S.B., pp. 134-149.
Catalog, “Proteins & Genes,” Novagen.
G.M. Bonora et al., “Structure of N-Tert-Butuyloxycarbonyl-D-leucyl-L-phenylalanylethanolamide,”J. Biol. Chem. 258:14725-14732 (1983).
Sieber and Iselin, “Selective acidolytische Spaltung von Aralkyloxycarbonyl-Aminoschutzgruppen,”Helv. Chim. Acta51:614-622 (1968).
V.K. Prasad et al., “Solid-phase Reagents for the Isolation and Protection of Carbonyl Compounds,”J.Ster. Bioch. 18:257-261 (1983).
Kanda et al., “New Potent Mitomycin Derivatives: Synthesis and Antitumor Activity of 7,7-(Ethylenedioxy)mitocins,”J. Med. Chem. 35:2781-2786.
A. Pilc et al., “N-Ethoxycarbony-2-ethocy-1,2-dihydroquinoline, An Irreversible Receptor Inactivator, as a Tool for Measurement of α-Adrenoceptor Occupancy In Vivo,”Eur. J. Pharm. 212:109-111 (1992).
J.W. Lown et al. “Mechanism of Action of 2-Haloethylnitrosoureas on Deoxyribonucleic Acid,”Bioch. Pharm. 34:1015-1024 (1985).
G.K. Watson et al., “Microbial Metabolism of the Pyridine Ring,”Biochem. J. 146:157-172 (1975).
E. Palomino et al., “Synthesis and in Vitro Evaluation of Some Modified 4-Thiopyrimidine Nucleosides for Prevention or Reversal of AIDS-Associated Neurological Disorders,”J. Med. Chem. 33:258-263 (1990).
Heikkila and Chattopadhyaya, “The 9-Fluorenylmethoxycarbonyl (Fmoc) Group for the Protection of Amino Functions of Cytidine, Adenosine, Guanosine and Their 2′-Deoxysugar Derivatives,”Acta Chem. Scand. B37:263-265 (1983).
Webb and Matteucci, “Hybridization triggered cross-linking of deoxyoligonucleotides,”Nucleic Acids Research14(19):7661-7674 (1986).
Beaucage and Caruthers, “Deoxynucleoside Phosphoramidites-A New Class of Key Intermediates for Deoxypolynucleotide Synthesis,”Tetrahed. Lett., 22(20):1859-1862 (1981).
Alvarado Gabriel G.
Chiarello Ronald H.
Liu Wing-Cheong
Medlen & Carroll LLP
Qian Celine
Syn Gen, Inc.
LandOfFree
Compositions and methods for labeling oligonucleotides does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Compositions and methods for labeling oligonucleotides, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Compositions and methods for labeling oligonucleotides will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3822101