Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2006-02-07
2006-02-07
Horlick, Kenneth R. (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S069100, C435S091100, C435S091510, C536S023100, C536S023500, C536S024330
Reexamination Certificate
active
06994963
ABSTRACT:
This invention pertains to a method for generating a pool of nucleic acid fragments useful for in vitro recombination and the creation of novel DNA sequences that encode desirable proteins or enzymes. The invention provides a defined mixture of nucleic acids and methods for use in the synthesis, mutagenesis, and recombination of nucleic acids. Nucleic acids may be synthesized by creating a nucleic acid extension ladder, annealing the extension ladder to template nucleic acids, and further extending the ladder of nucleic acids. The invention also relates to methods for performing repeated cycles of synthesis for the purpose of mutagenesis or recombination, methods for producing mutant peptides and proteins from the mutagenized or recombined nucleic acids, and methods for selecting a peptide, polypeptide or protein having altered biological activities.
REFERENCES:
patent: 4865968 (1989-09-01), Orgel et al.
patent: 5106585 (1992-04-01), Minami et al.
patent: 5679512 (1997-10-01), Laney et al.
patent: 5723323 (1998-03-01), Kauffman et al.
patent: 5741676 (1998-04-01), Fuller
patent: 5747298 (1998-05-01), Hong et al.
patent: 5830655 (1998-11-01), Monforte et al.
patent: 5965408 (1999-10-01), Short
patent: 6087095 (2000-07-01), Rosenthal et al.
patent: 6117679 (2000-09-01), Stemmer
patent: 6132970 (2000-10-01), Stemmer
patent: 6153410 (2000-11-01), Arnold et al.
patent: 6159687 (2000-12-01), Vind
patent: 6165793 (2000-12-01), Stemmer
patent: 6177263 (2001-01-01), Arnold et al.
patent: 6180406 (2001-01-01), Stemmer
patent: 6506603 (2003-01-01), Stemmer
patent: 6534292 (2003-03-01), Volkov
patent: WO 97/20078 (1997-06-01), None
patent: WO 98/01581 (1998-01-01), None
patent: WO 98/05765 (1998-02-01), None
patent: WO 98/27230 (1998-06-01), None
patent: WO 98/32845 (1998-07-01), None
patent: WO 98/41622 (1998-09-01), None
patent: WO 98/41623 (1998-09-01), None
patent: WO 98/41653 (1998-09-01), None
patent: WO 98/42728 (1998-10-01), None
patent: WO 98/42832 (1998-10-01), None
patent: WO 98/58080 (1998-12-01), None
patent: WO 99/15698 (1999-04-01), None
patent: WO 99/20768 (1999-04-01), None
patent: WO 99/29882 (1999-06-01), None
patent: WO 99/47536 (1999-09-01), None
patent: WO 00/42561 (2000-07-01), None
Altschul et al., “Basic Local Alignment Search Tool,”J. Mol. Biol.215:403-410, 1990.
Ambrose et al., “DNA Sequencing: Chemical Methods,”152:522-538, 1987.
Arkin et al., “An Algorithm for protein engineering: Simulations of recursive ensemble mutagenesis,”PNAS USA89:7811-7815, 1992.
Barcak, et al., “A method for unidirectional deletion mutagenesis with application to nucleotide sequencing and preparation of gene fusions,”Gene,49:119-128, 1986.
Breaker et al., “Self-Incorporation of Coenzymes by Ribozymes,”J. Mol Evol.,40:551-558, 1995.
Caldwell and Joyce, “Mutagenic PCR,”PCR Methods and Applications,3:S136-S140, 1994.
Carbonelli et al., “A placid vector for isolation of strong promoters inEschirichia coli,” FEMS Microbiol Lett.,177:75-82, 1999.
Chandler et al., “RNA splicing specificity determined by the coordinated action of RNA recognition motifs in SR proteins,”Proc Natl Acad Sci U S A.,94:3596-3601, 1997.
Chang et al., “Evolution of a cytokine using DNA family shuffling,”Nature Biotechnology,17:793-797, 1999.
Chapman and Szostak, “Isolation of a ribozyme with 5′- 5′ ligase activity,”Chem Biol.2:325-333, 1995.
“Light based scissors cleave DNA,”Chemical and Engineering News,Sep. 13, p 40, 1999.
Chen and Okayama, “High-Efficiency Transformation of Mammalian Cells by Plasmid DNA,”Mol. Cell. Biol.,7:2745-2752, 1987.
Chowrira et al., “In Vitro and in Vivo Comparison of Hammerhead, Hairpin, and Hepatitis Delta Virus Self-processing Ribozyme Cassettes,”J. Biol. Chem.,269:25856-25864, 1994.
Cocea, “Duplication of a Region in the Multiple Cloning Site of a Plasmid Vector to Enhance Cloning-Mediated Addition of Restriction Sites to a DNA Fragment,”Biotechniques,23:814-816, 1997.
Crameri et al., “DNA shuffling of a family of genes from diverse species accelerates directed evolution,”Nature,391:288-291, 1998.
Crameri et al., “Improved Green Fluorescent Protein by Molecular Evolution Using DNA Shuffling,”Nature Biotechnology,14:315-319, 1996.
Current Protocols in Molecular Biology.Ed. F. M. Ausubel et al., vol. 1, 1996, Table of Contents.
Eun,“Enzymology Primer for Recombinant DNA Technology,”Academic Press,3:215-220, 1996.
Fechheimer et al., “Transfection of mammalian cells with plasmid DNA by scrape loading and sonication loading,”Proc. Natl. Acad. Sci., USA84:8463-8467, 1987.
Foder et al., “Light-Directed, Spatially Addressable Parallel Chemical Synthesis,”Science,251:767-773, 1991.
Fraley and Fornari Kaplan, “Entrapment of a bacterial plasmid in phospholipid vesicles: Potention for gene transfer,”Proc. Nat'l. Acad. Sci. USA,76:3348-3352, 1979.
Gish and Eckstein, “DNA and RNA sequencing utilizing phosphorothioate chemistry,”NAR Symp. Ser.,8:253-256, 1987.
Gopal, “Gene Transfer Method for Transicnt Gene Expression, Stable Transformation, and Cotransformation of Suspension Cell Cultures,”Mol. Cell. Biol.,5:1188-1190, 1985.
Graham and Van Der Eb, “A New Technique for the Assay of Infectivity of Human Adenovirus 5 DNA,”Virology,52:456-467, 1973.
Kaeppler et al., “Silicon carbide fiber-mediated DNA delivery into plant cells,”Plant Cell Reports,9: 415-418, 1990.
Kaneda et al., “Increased Expression of DNA Cointroduced with Nuclear Protein in Adult Rat Liver,”Science,243:375-378, 1989.
Kato et al., “Expression of Hepatitis B Virus Surface Antigen in Adult Rat Liver,”J. Biol. Chem.,266:3361-3364, 1991.
Labeit et al., “A New Method of DNA Sequencing Using Deoxynucleoside α-Thiotriphosphates,”DNA5:173-177, 1986.
Lee et al., “Ribozyme-catalyzed tRNA aminoacylation,”Nat Struct Biol.,7:28-33, 2000.
Leung et al., “A Method for Random Mutagenesis of a Defined DNA Segment Using a Modified Polymerase Chain Reaction,”Technique,1:11-15, 1989.
Lieber and Strauss, “Selection of Efficient Cleavage Sites in Target RNAs by Using a Ribozyme Expression Library,”Mol. Cell. Biol.,15:540-551, 1995.
Lohse and Szostak, “Ribozyme-catalysed amino-acid transfer reactions,”Nature.30:381:442-444, 1996.
Longo et al., “Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions,”Gene,93:125-128, 1990.
Lorsch and Szostak, “Kinetic and Thermodynamic Characterization of the Reaction Catalyzed by a Polynucleotide Kinase Ribozyme,”Biochemistry,34:15315-15327, 1995.
Macejak and Sarnow, “Internal initiation of translation mediated by the 5′ leader of a cellular mRNA,”Nature,353:90-94, 1990.
Maxam and Gilbert, “Sequencing End-Labeled DNA with Base-Specific Chemical Cleavages,”Methods Enzymology,65:499-560, 1980.
Messing and Vieira, “A new pair of M13 vectors either DNA strand of double-digest restriction fragments,”Gene,19:269-276, 1982.
Moore and Arnold, “Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents,”Nature Biotechnology,14:458-467, 1996.
Moore et al., “Strategies for the in vitro Evolution of Protein Function: Enzyme Evolution by Random Recombination of Improved Sequences,”J. Molecular Biol.,272:336-347, 1997.
Nicolau and Sene, “Lipsome-Mediated DNA Transfer in Eukaryotic Cells,”Biochem. Biophys. Acta,721:185-190, 1982.
Nicolau et al., “Liposomes as Carriers for in Vivo Gene Transfer and Expression,” 149:157-176, 1987.
Nixon et al., “Hybrid enzymes: manipulating enzyme design,”Trends in Biotech.,16:258-264, 1989.
Ohuchi et al., “In vitro method for the generation of protei
Ellington Andrew D.
Murphy George L.
Setterquist Robert A.
Ambion Inc.
Fulbright & Jaworski
Horlick Kenneth R.
Wilder Cynthia B.
LandOfFree
Methods for recombinatorial nucleic acid synthesis does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Methods for recombinatorial nucleic acid synthesis, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods for recombinatorial nucleic acid synthesis will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3695243