Chemistry: molecular biology and microbiology – Process of mutation – cell fusion – or genetic modification – Introduction of a polynucleotide molecule into or...
Reexamination Certificate
2000-08-25
2002-11-12
Guzo, David (Department: 1636)
Chemistry: molecular biology and microbiology
Process of mutation, cell fusion, or genetic modification
Introduction of a polynucleotide molecule into or...
C435S410000, C435S469000, C435S470000, C514S04400A, C536S023100, C536S026600
Reexamination Certificate
active
06479292
ABSTRACT:
1. FIELD OF THE INVENTION
The invention concerns single-stranded oligodeoxynucleotides, certain derivatives thereof and methods of their use for introducing a predetermined change at a predetermined location in a target gene in a living cell. The cell can be a mammalian, insect, fish, worm or avian cell, either in an artificial culture medium or in an organism, a bacterial cell or a plant cell. The target gene can be a chromosomal gene or an extrachromosomal gene, i.e., on a bacterial artificial chromosome.
2. BACKGROUND OF THE INVENTION
Techniques of making a predetermined change at a predetermined location in a target nucleic acid sequence of a cell have been described. These techniques utilize the cell's enzymes that concern DNA repair and homologous recombination. In these techniques an oligonucleotide or oligonucleotide analog is synthesized that contains two regions that have the sequence of the target gene that flank a region, termed a “mutator region”, that differs from the target gene. In this application such oligonucleotides and analogs will be generically termed “mutational vectors”. Such mutational vectors can introduce predetermined genetic changes into a target gene by a mechanism that is believed to involve homologous recombination and/or nucleotide excision and repair.
U.S. Pat. Nos. 5,565,350 and No. 5,731,181 to Kmiec describe mutational vectors that contain complementary strands wherein a first strand comprises ribonucleotide analogs that form Watson-Crick base pairs with deoxyribonucleotides of a second strand. U.S. Pat. No. 6,004,804 to Kumar and Metz describes certain improvements in duplex mutational vectors, including a variant in which the mutator region is present on only one of the two strands. The use of Kmiec type mutational vectors in mammalian systems is described in U.S. Pat. No. 5,760,012 and in conjunction with macromolecular carriers in International Patent Publication WO 98/49350 to Kren et al., and in related U.S. patent application Ser. No. 09/108,006. Additional descriptions of the use of Kmiec type mutational vectors can be found in Cole-Strauss et al., 1996, Science 273:1386; Kren et al., 1998, Nature Med. 4:285; and Bandyopadhyay et al., 1999, J. Biol. Chem. 274:10163.
The use of Kmiec type mutation vectors in plant cells is described in International Patent Publications WO 99/25853 to Pioneer Hi-Bred International, WO 99/07865 to Kimeragen, Inc. and WO 98/54330 to Zeneca Ltd. Scientific publications that describe the use of Kmiec type vectors in plants include Beetham et al., 1999, Proc. Natl. Acad. Sci. USA 96:8774 and Zhu, et al.,1999, Proc. Natl. Acad. Sci. USA 96:8768.
The use of Kmiec type mutational vectors and variants thereof, which are double stranded, is described in U.S. Pat. No. 6,004,804 to Kumar and Metz. The application of Kumar and Metz teaches, inter alia, that Kmiec type vectors and variants thereof can be used in bacterial cells.
The use of single stranded oligodeoxynucleotides as mutational vectors to effect changes in a chromosomal gene in the yeast, S. cerevisiae, was described in reports from the laboratory of Dr. F. Sherman, Yale University. Moerschell et al., 1988, Proc. Natl. Acad. Sci. USA, 85:524-528 and Yamamoto et al., 1992, Yeast 8:935-948. The optimum length of the mutational vectors used in these studies was 50 nucleotides.
An isolated report of the use of a 160 nucleotide single and double stranded polynucleotide to attempt to make alterations in a chromosomal gene can be found at Hunger-Bertling, 1990, Mol. Cell. Biochem. 92:107-116. The results for single stranded polynucleotides were ambiguous because only the product of the experiments using double-stranded polynucleotides were analyzed.
The use of single stranded DNA fragment of 488 base pairs to make specific genetic changes in the cystic fibrosis transmembrane conductance regulator gene has been reported by Goncz et al., 1998, Hum. Mol. Genetics 7:1913; and Kunzelmann et al., 1996, Gene Ther. 3:859.
Single stranded oligodeoxynucleotides of about 40 nucleotides in length in mammalian cells were used as a control for studies of episomal genes in which the oligodeoxynucleotide was covalently linked to a triplex forming oligonucleotide and that the oligodeoxynucleotide alone resulted in rates of predetermined genetic change of the episomal gene of about 1 per 5×10
4
, or fewer. Chan et al., 1999, J. Biol. Chem. 74:11541. An earlier report of the use of single-stranded oligodeoxynucleotide to make predetermined changes in an episomal gene in a mammalian cell is found in Campbell et al., 1989, The New Biologist 1:223.
One aspect of the invention concerns oligodeoxynucleotides that have been modified by the attachment of an indocarbocyanine dye. Indocarbocyanine dyes are known as excellent fluorophores. The synthesis of blocked indocarbocyanine &bgr; cyanoethyl N,N-diisopropyl phosphoroamidites that are suitable for use in solid phase nucleotide synthesis is described in U.S. Pat. Nos. 5,556,959 and No. 5,808,044.
A second aspect of the invention concerns a composition comprising a single stranded oligonucleotide encoding a predetermined genetic change and a macromolecular carrier that comprises a ligand for a receptor on the surface of the target cell. A composition comprising a poly-L-lysine, a ligand for the asialoglycoprotein receptor and an antisense oligodeoxynucleotide of between 21 and 24 nucleotides is described in International Patent Publication WO 93/04701.
A third aspect of the invention concerns a modification of a oligodeoxynucleotide by the attachment of a 3′—3′ linked nucleotide. U.S. Pat. No. 5,750,669 teaches such a modified oligodeoxynucleotide.
Citation or identification of any reference in Section 2, or any section of this application shall not be construed as an admission that such reference is available as prior art to the present invention.
3. SUMMARY OF THE INVENTION
The present invention is based on the unexpected discovery that single-stranded oligodeoxynucleotides, particularly when appropriately modified or placed in a composition with a suitable macromolecular carrier, can be as or more effective in making predetermined genetic changes to target genes in cells as the prior art, i.e., Kmiec type mutational vectors. A single stranded oligodeoxynucleotide suitable for use according to the present invention is termed hereafter a Single-Stranded Oligodeoxynucleotide Mutational Vector or a SSOMV.
In one embodiment the invention provides for a composition for use in making changes to the chromosomal genes of animal, e.g. mammalian, cells consisting of the oligodeoxynucleotide encoding the genetic change and a macromolecular carrier. The carrier can be either a polycation, an aqueous-cored lipid vesicle or a lipid nanosphere. In a further embodiment that is suitable for in vivo use, the carrier further comprises a ligand that binds to a cell-surface receptor that is internalized such as a lignad for a clathrin-coated pit receptor, e.g., the asialoglycoprotein receptor, the folic acid receptor or the transferin receptor. In preferred embodiments the oligodeoxynucleotide is modified by the attachment of 3′ and 5′ blocking substituents such as a 3′—3′ linked cytosine nucleotide and a 5′ linked indocarbocyanine dye. In an alternative embodiment the modification can consist of the replacement of the 3′ most and/or 5′ most internucleotide phosphodiester linkage with a non-hydrolyzeable linkage such as a phosphorothioatediester linkage or a phosphoramidate linkage.
In a second embodiment the invention provides for the modification of the 3′ and 5′ end nucleotides of the oligodeoxynucleotide that encodes the predetermined genetic change. The invention is further based on the unexpected discovery that certain such modifications do not block the effectiveness of the oligodeoxynucleotide to produce genetic changes. One such embodiment is the combination of a 3′—3′ linked cytosine nucleotide and a 5′ linked indocarbocyanine dye. So modified, the
Frank Bruce L.
Metz Richard A.
Walther Debra M.
Guzo David
Leffers, Jr. Gerald G.
Pennie & Edmonds LLP
ValiGen (US), Inc.
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