Chimeric mutational vectors

Details Chimeric mutational vectors Chimeric mutational vectors

2001-04-03

2003-07-01

Guzo, David (Department: 1636)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C536S022100, C536S023100, C435S440000, C435S471000, C435S485000, C435S488000, C435S243000, C435S252100, C435S252300, C435S320100

Reexamination Certificate

active

06586184

ABSTRACT:

1. FIELD OF THE INVENTION
The invention concerns the use of duplex oligonucleobase compounds (hereafter “duplex mutational vectors”) to specifically make alterations in the sequence of a DNA in a cell. In one embodiment the invention concerns compounds and methods of their use to make specific genetic alterations in the genome and in episomes (plasmids) of target prokaryotic cells. In a further embodiment the invention concerns methods of using bacterial cells to develop more efficient duplex mutational vectors. The structure of the duplex mutational vector (DMV) is designed so that genetic exchange between the DMV and the target gene occurs, i.e., a sequence contained in the DMV replaces the sequence of the target gene. In still further embodiments the invention concerns specific generic structures of DMV.
2. BACKGROUND OF THE INVENTION
U.S. Pat. No. 5,565,350, issued Oct. 15, 1996, and U.S. Pat. No. 5,731,181, issued Mar. 24, 1998 by E. B. Kmiec, described Chimeric Mutational Vectors (CMV), i.e., vectors having both DNA-type and RNA-type nucleobases for the introduction of genetic changes in eukaryotic cells. Such CMV were characterized by having at least 3 contiguous base pairs wherein DNA-type and RNA-type nucleobases are Watson-Crick paired with each other to form a hybrid-duplex. A CMV designed to repair a mutation in the gene encoding liver/bone/kidney type alkaline phosphatase was reported in Yoon, K., et al., March 1996, Proc. Natl. Acad. Sci. 93, 2071. The alkaline phosphatase gene was transiently introduced into CHO cells by a plasmid. Six hours later the CMV was introduced. The plasmid was recovered at 24 hours after introduction of the CMV and analyzed. The results showed that approximately 30 to 38% of the alkaline phosphatase genes were repaired by the CMV.
A CMV designed to correct the mutation in the human &bgr;-globin gene that causes Sickle Cell Disease and its successful use was described in Cole-Strauss, A., et al., 1996, Science 273:1386. A CMV designed to create a mutation in a rat blood coagulation factor IX gene in the hepatocyte of a rat is disclosed in Kren et al., 1998, Nature Medicine 4, 285-290. An example of a CMV having one base of a first strand that is paired with a non-complementary base of a second strand is shown in Kren et al., June 1997, Hepatology 25, 1462.
U.S. patent application Ser. No. 08/640,517, filed May 1, 1996 now U.S. Pat. No. 5,760,012, by E. B. Kmiec, A. Cole-Strauss and K. Yoon, published as WO97/41141, Nov. 6, 1997, and application Ser. No. 08/906,265 now U.S. Pat. No. 5,888,983, filed Aug. 5, 1997, disclose methods and CMV that are useful in the treatment of genetic diseases of hematopoietic cells, e.g., Sickle Cell Disease, Thalassemia and Gaucher Disease.
The above-cited scientific publications of Yoon, Cole-Straauss and Kren describe CMV having two 2′-O-methyl RNA segments separated by an intervening DNA segment, which were located on the strand opposite the strand having the 5′ end nucleotide. U.S. Pat. No. 5,565,350 described a CMV having a single segment of 2′-O-methylated RNA, which was located on the chain having the 5′ end nucleotide. An oligonucleotide having complementary deoxyribonucleotides and a continuous segment of unmodified ribonucleotides on the strand opposite the strand having the 5′ end nucleotide was described in Kmiec, E. B., et al., 1994, Mol. and Cell. Biol. 14:7163-7172. The sequence of the strand was derived from the bacteriophage M13mp19,
The use of single stranded oligonucleotides to introduce specific mutations in yeast are disclosed in Yamamoto, T., et al., 1992, Genetics 131, 811-819. The oligonucleotides were between about 30 and 50 bases. Similar results were reported by Campbell, C. R., et al., 1989, The New Biologist, 1, 223-227. Duplex DNA fragments of about 160 base pairs in length have been reported to introduce specific mutations in cultured mammalian cells. Hunger-Bertling, K., et al., 1990, Molecular and Cellular Biochemistry 92, 107-116.
Applicants are aware of the following provisional applications that contain teaching with regard to uses and delivery systems of recombinagenic oligonucleotides: By Steer et al., Ser. Nos. 60/045,288 filed Apr. 30, 1997; 60/054,837 filed Aug. 5,1997; 60/064,996, filed Nov. 10, 1997; and by Steer & Roy-Chowdhury et al., Ser. No. 60/074,497, filed Feb. 12, 1998, entitled “Methods of Prophylaxis and Treatment by Alteration of APO B and APO E Genes.”


REFERENCES:
patent: 5565350 (1996-10-01), Kmiec
patent: 5731181 (1998-03-01), Kmiec
patent: 5760012 (1998-06-01), Kmiec et al.
patent: 5872232 (1999-02-01), Cook et al.
patent: 5948653 (1999-09-01), Pati et al.
patent: 6004804 (1999-12-01), Kumar et al.
patent: 6010907 (2000-01-01), Kmiec et al.
patent: WO 97/26334 (1997-07-01), None
Campbell et al., 1989, “Homologous recombination involving small single-stranded oligonucleotides in human cells”, The New Biologist 1:223-227.
Cole-Strauss et al., 1996, “Correction of the mutation responsible for sickle cell anemia by an RNA-DNA oligonucleotide”, Science 273(5280):1386-9.
Durand et al., 1990, “Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability”, Nucleic Acids Res. 18(21):6353-9.
Gamper et al., 1993, “Facile preparation of nuclease resistant 3' modified oligodeoxynucleotides”, Nucleic Acids Res. 21(1):145-50.
Hosoda et al., 1990, “An F factor based cloning system for large DNA fragments”, Nucleic Acids Res. 18(13):3863-9.
Hunger-Bertling et al., 1990, “Short DNA fragments induce site specific recombination in mammalian cells”, Mol Cell Biochem. 92(2):107-16.
Ioannou et al., 1994, “A new bacteriophage P1-derived vector for the propagation of large human DNA fragments”, Nat. Gen. 6:85-89.
Kotani et al., 1996, “RNA facilitates RecA-mediated DNA pairing and strand transfer between molecules bearing limited regions of homology”, Mol Gen Genet 250(5):626-34.
Kren et al., 1998, “In vivo site-directed mutagenesis of the factor IX gene by chimeric RNA/DNA oligonucleotides”, Nat Med. 4(3):285-90.
Letsinger et al., 1995, “Use of stilbenedicarboxamide bridge in stabilizing, monitoring, and photochemically altering folded conformations of oligonucleotides”, J. Am. Chem. Soc. 117:7323-7328.
Messerle et al., 1997, “Cloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome”, Proc Natl Acad Sci U S A 94(26):14759-63.
Shizuya et al., 1992, “Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA inEscherichia coliusing an F-factor-based vector”, Proc Natl Acad Sci U S A 89(18):8794-7.
Wang et al., 1995, “Relative stabilities of triple helices composed of combinations of DNA, RNA and 2'-O-methyl-RNA backbones: chimeric circular oligonucleotide as probes”, Nucleic Acids Research, vol. 23, No. 7, pp. 1157-64 (1995).
Yamamoto et al., 1992, “Strand-specificity in the transformation of yeast with synthetic oligonucleotides”, Genetics 131(4):811-9.
Yamamoto et al., 1992, “Parameters affecting the frequencies of transformation and co-transformation with synthetic oligonucleotides in yeast”, Yeast 8(11):935-48.
Yang et al., 1997, “Homologous recombination based modification inEscherichia coliand germline transmission in transgenic mice of a bacterial artificial chromosome”, Nat Biotechnol 15(9):859-65.
Yoon et al., 1996, “Targeted gene correction of episomal DNA in mammalian cells mediated by a chimeric RNA.DNA oligonucleotide”, Proc Natl Acad Sci U S A 93(5):2071-6.

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