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Compositions comprising genome segments and methods of using the sameRelated Patent Categories: Drug, Bio-affecting And Body Treating Compositions, Designated Organic Active Ingredient Containing (doai), O-glycoside, , Nitrogen Containing Hetero Ring, Polynucleotide (e.g., Rna, Dna, Etc.)Compositions comprising genome segments and methods of using the same description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20070225244, Compositions comprising genome segments and methods of using the same. Brief Patent Description - Full Patent Description - Patent Application Claims
CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application claims priority to U.S. Provisional Application No. 60/174,155 filed Jan. 3, 2000, which is incorporated herein by reference. FIELD OF THE INVENTION [0002] The present invention relates to compositions and methods of treating individuals with diseases and disorders associated with genetic mutations. According to the present invention, DNA is administered to individuals who take it up and replace DNA with mutated sequences with DNA with non-mutated sequences or substitute existing set of alleles to a different one. The present invention also relates to compositions and methods for preventing and treating infections, allergies, transplant rejections and infertility. BACKGROUND OF THE INVENTION [0003] Every cell of an organism contains genomic DNA that keeps encoded information about all proteins of all cells of the organism and eventually about the whole organism and its development. Initially this genomic DNA is identical in all cells of an organism. But as the organism grows genomic DNA of every cell becomes subjected to mutational pressure due to environmental factors and mistakes of cellular replication and repair machinery. The known cellular DNA repair mechanisms replace damaged or incorrect DNA bases and rejoin ends of DNA after single-strand and double-strand breaks immediately after mutational events. They can also employ the second DNA chain as a template. When the damage is rather long and affects both DNA chains its repair becomes problematic and the damage results in mutation. The double-strand break repair mechanism can itself be a source of mutations (Pfeifer, P., The mutagenic potential of DNA double-strand break repair, 1998, 96-97, 119-129). As mutations are accumulated in the cellular genome they can cause malfunction of some cells or cancerous transformation. [0004] Environmental mutagenic factors and errors of cellular replication and repair are sources of somatic cell mutations. It has been suggested that gradual accumulation of mutations in cells can cause multi-step cancer transformation. Somatic mutations are considered to be the main cause of aging. Mutations may also induce development of some hereditary associated diseases such as cardio-vascular diseases, high blood pressure, rheumatoid arthritis, and diabetes. [0005] The genetic, multi-mutational nature of cellular cancer transformation and cancer itself suggests that methods of cancer therapy should be directed to the cause of the disease and particularly targeted to the treatment of mutations. Methods for fixing definite point mutations in cells have been suggested (U.S. Pat. No. 5,795,972 issued to Kmiec on Aug. 18, 1998, which is incorporated herein by reference) but according to the method, mutations must be precisely identified before each treatment. Because not a single mutation has been 100% proven to cause a cancer, the development of these methods requires additional fine and time-consuming research. There is a need for methods which can be applied based upon the current knowledge underlying the causes of cancer. [0006] Applying DNA fragments locally has been suggested for treatment of precancerous conditions in skin of patients and for tanning stimulation (U.S. Pat. No. 5,955,059 issued to Gilchrest, et al., on Sep. 21, 1999; and U.S. Pat. No. 5,470,577 issued to Gilchrest, et al., Nov. 8, 1995, both of which are incorporated herein by reference). No sequences or sources of DNA are specified. Rather, the patent suggests that `any appropriate sources` DNA natural or synthetic, for example, salmon DNA with the length from 200 to mononucleotides and nucleosides including dimers, the most potent agents in their tests can be used. [0007] Another method to activate DNA repair in cells is offered including delivery of enzymes participating in DNA repair into skin cells (U.S. Pat. No. 5,352,458 issued to Yarosh, Oct. 4, 1994; and U.S. Pat. No. 5,302,389 issued to Kripke, et. al., Apr. 12, 1994, both of which are incorporated herein by reference). However the latter methods do not suggest fixing of already established or inherited mutations. [0008] There remains a need for methods of correcting genetic mutations. There remains a need for treating individuals who have diseases and disorders associated with genetic mutations. There remains a need to replace undesirable alleles with desirable alleles. There is a further need for methods for inducing tolerance to prevent transplant rejection. There is a further need for methods for inducing tolerance to treat and prevent allergies. There is a need for methods for increasing fertility. SUMMARY OF THE INVENTION [0009] The present invention arises from the surprising discovery that when an entire genome is administered to an individual in the form of a plurality of polynucleotide molecules that are fragments of genomic DNA, the polynucleotide molecules will circulate, be taken up by cells and translocate to the nucleus of the cells where they will recombine by homologous recombination with the genomic DNA of the cell. Accordingly, genetic defects can be corrected by administering an entire genome to an individual in the form of polynucleotide molecules that are fragments of genomic DNA that are free of the genetic defect. Individuals with diseases and disorders associated with genetic mutations can be effectively treated by the present invention. [0010] Human genomic DNA fragments are used for treating cancer and other diseases caused by mutations. Nucleic acid molecules derived from "healthy" donor DNA is administered to the patient. The nucleic acid molecules correct mutational changes in cells via homologous recombination with mutated genomic sequences. This mechanism modifies allelic genes and in this way an antigenic structure of organism in accordance with composition of administered nucleic acid molecules. The present invention is useful for induction of immunological tolerance at transplantation or pregnancy. [0011] The present invention relates to methods of treating individuals who have diseases or disorders associated with a genetic mutation or undesirable allele in genomic DNA and to methods of preventing individuals from developing diseases or disorders associated with a genetic mutation or undesirable allele in genomic DNA. According to the invention a segment of genomic DNA that has a mutated sequence or undesirable allele is replaced with a corresponding segment of DNA that has a non-mutated sequence or desirable allele. The methods comprise the step of administering to the individual an effective amount of a plurality of polynucleotide molecules that are free of vector sequences. The plurality of polynucleotide molecules collectively comprises an essentially complete genome in polynucleotide molecules having about 100-3000 nucleotides, and includes a polynucleotide molecule which comprises a non-mutated sequence or desirable allele corresponding to the genetic mutation or undesirable allele in the genomic DNA of the cell in the individual. At least some of the plurality of polynucleotide molecules including the polynucleotide molecule which comprises the non-mutated sequence or desirable allele are taken up by the cell of the individual which has the genetic mutation or undesirable allele in genomic DNA, transported to the nucleus of the cell, and recombine with the genomic DNA of the cell by homologous recombination. The mutated sequence or undesirable allele of genomic DNA of the cell is replaced by the non-mutated sequence or desirable allele to correct the genetic mutation in the genomic DNA or incorporate the desirable allele into the genomic DNA. [0012] The present invention relates to methods of inducing tolerance and preventing transplant rejection in an individual comprising the steps of administering to the individual an effective amount of a plurality of polynucleotide molecules that are free of vector sequences. The plurality of polynucleotide molecules collectively comprises an essentially complete genome of the donor in polynucleotide molecules having about 100-3000 nucleotides. At least some of the plurality of polynucleotide molecules are taken up by the cell of the individual, are transported to the nucleus of the cell, and recombine with the genomic DNA of the cell by homologous recombination. The genomic DNA of the individual is replaced by genomic DNA of the donor and tolerance is induced and transplant rejection is reduced in the individual. [0013] The present invention relates to methods of inducing tolerance and treating allergies in an individual comprising the steps of administering to the individual an effective amount of a plurality of polynucleotide molecules that are free of vector sequences. The plurality of polynucleotide molecules collectively comprises an essentially complete genome of the donor in polynucleotide molecules having about 100-3000 nucleotides. At least some of the plurality of polynucleotide molecules are taken up by the cell of the individual, are transported to the nucleus of the cell, and recombine with the genomic DNA of the cell by homologous recombination. The genomic DNA of the individual is replaced by genomic DNA of the donor and tolerance is induced and allergies are reduced in the individual. [0014] The present invention further relates to methods of increasing fertility in a woman. The methods comprise the step of administering to the woman an effective amount of a plurality of polynucleotide molecules that are free of vector sequences. The plurality of polynucleotide molecules collectively comprises an essentially complete genome of a prospective father in polynucleotide molecules having about 100-3000 nucleotides. At least some of the plurality of polynucleotide molecules are taken up by cells of the woman, transported to the nucleus of the cell, and recombine with the genomic DNA of the cell by homologous recombination. Genomic DNA of the woman is replaced by genomic DNA of the prospective father and fertility is improved in the woman. [0015] The present invention relates to methods of preventing or reducing graft versus host disease in a recipient comprising the steps of administering to the donor an effective amount of a plurality of polynucleotide molecules that are free of vector sequences. The plurality of polynucleotide molecules collectively comprises an essentially complete genome of the recipient in polynucleotide molecules having about 100-3000 nucleotides. At least some of the plurality of polynucleotide molecules are taken up by the cells of the recipient, transported to the nucleus of the cell, and recombine with the genomic DNA of the cell by homologous recombination. The genomic DNA of the donor is replaced by genomic DNA of the recipient. Following transplantation/grafting, the level of graft versus host disease is reduced or prevented. [0016] The present invention relates to methods of introducing one or more desirable alleles into livestock which contains undesirable alleles comprising the steps of administering to the livestock an effective amount of a plurality of polynucleotide molecules that are free of vector sequences. The plurality of polynucleotide molecules collectively comprises an essentially complete genome of the livestock species in polynucleotide molecules having about 100-3000 nucleotides including the desirable alleles. At least some of the plurality of polynucleotide molecules are taken up by the cells animal, transported to the nucleus of the cell, and recombine with the genomic DNA of the cell by homologous recombination. The undesirable alleles in the genomic DNA of the animal is replaced by the desirable alleles. [0017] The present invention relates to an apparatus for doing large scale PCR preparations. The apparatus comprises a reaction tube that has an inner diameter of 3 mm or more, at least one pump for continuously supplying of reagents to the reaction tube, four temperature chambers and a collection vessel. The reagents are combined and enter the reaction tube by action of the pump. The reaction tube comprises a series of reaction tube lengths which alternately pass through each of the four temperature chambers to produce a cycle segment, such that a length of the reaction tube passes through the first temperature chamber, a length of the reaction tube passes through the second temperature chamber, a length of the reaction tube passes through the third first temperature chamber, a length of the reaction tube passes through the fourth temperature chamber to produce a cycle segment. The reaction tube comprises at least twenty consecutive cycle segments and is connected to the collection vessel following the last cycle segment. [0018] The present invention relates to pharmaceutical compositions that comprises, in a pharmaceutically acceptable carrier, a plurality of polynucleotide molecules which collectively comprise an essentially complete genome in polynucleotide molecules having about 100-3000 nucleotides. BRIEF DESCRIPTION OF THE DRAWINGS [0019] FIG. 1A shows changes in specific protein expression in human cancer cells induced by preparations of human DNA. Three assays were run on each of three cancer cell types (human breast cancer cells BT474, ovarian carcinoma cells OVCAR5 and promyelocytic leukemia cells HL60) and expression was tested of proteins associated with cancer, erbB2 for BT474 and OVCAR5 cells, c-myc for HL60 cells and cyclin D1 for all three cell types. FIG. 1A contains six autoradiograms; in each lane C designates the control human breast cancer cells BT474, ovarian carcinoma cells OVCAR5 and promyelocytic leukemia cells HL60; each lane D designates the same cells treated for 2 weeks with DNA preparations (2 .mu.g/well); each lane Ch designates the same cells treated for 2 weeks with chromatin preparations (2 .mu.g of DNA per well). Equal protein amounts of cell lysates were electrophoresed in SDS-PAAG and transferred to nitrocellulose membranes by Western blotting procedure. The membranes were incubated with specific antibodies to proteins Erb-B2, C-Myc and Cyclin D1, washed in buffer and incubated with secondary antibodies conjugated with HRP according to protocols of Santa Cruz Biotech, Co. The membranes were then washed and developed with Luminol reagent and exposed to X-ray film. FIG. 1A shows specific protein expression, X-ray films Continue reading about Compositions comprising genome segments and methods of using the same... 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