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Title:
SYNTHETIC AAV GENOMES FOR IMPROVED GENE DELIVERY
Document Type and Number:
WIPO Patent Application WO/2023/225455
Kind Code:
A2
Abstract:
Disclosed herein are methods for producing synthetic adeno-associated viral (AAV) genomes for improved gene delivery. The present disclosure also includes synthetic AAV genomes with no payload size limitation and capable of accommodating expression cassettes of any size. Also disclosed herein are compositions and methods for delivering a synthetic AAV genome to a cell for treat one or more disease or conditions in a subject.

Inventors:
CHAVEZ CHRISTOPHER (US)
Application Number:
PCT/US2023/066873
Publication Date:
November 23, 2023
Filing Date:
May 11, 2023
Export Citation:
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Assignee:
VISGENX INC (US)
International Classes:
C12N15/86; A61K48/00
Attorney, Agent or Firm:
FULLER, Michael L. (US)
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Claims:
WHAT IS CLAIMED IS: 1. A method for producing synthetic adeno-associated viral (AAV) genomes for improved gene delivery, comprising: cloning an expression cassette into a first AAV plasmid and into a second AAV plasmid, wherein the first AAV plasmid comprises a 5’ inverted terminal repeat (ITR) sequence and a truncated 3’ ITR sequence, and wherein the second AAV plasmid comprises a 3’ ITR sequence and a truncated 5’ ITR sequence; contacting the first AAV plasmid and the second AAV plasmid with at least one restriction enzyme; heating a solution comprising the first AAV plasmid and the second AAV plasmid, thereby providing a first DNA segment with a single-stranded DNA overhang portion from the first AAV plasmid and a second DNA segment with a complementary single-stranded DNA overhang portion from the second AAV plasmid, wherein the first DNA segment further comprises a 5’ ITR sequence and the single-stranded DNA overhang portion of the first DNA segment comprises a truncated 3’ ITR sequence, and wherein the second DNA segment further comprises a 3’ ITR sequence and the single-stranded DNA overhang portion comprises a truncated 5’ ITR sequence; and cooling the solution so that the single-stranded DNA overhang portion of the first DNA segment hybridizes with the complementary single-stranded DNA overhang portion of the second DNA segment to form a synthetic AAV genome. 2. The method of claim 1, wherein the method further comprises adding a DNA ligase to the solution. 3. The method of claim 1 or claim 2, wherein the method further comprises adding an exonuclease to the solution. 4. The method of any of claims 1-3, wherein the method further comprises applying the solution to a DNA purification column; and eluting the synthetic AAV genome.

5. The method of any one of claims 1 to 4, wherein the 5’ ITR sequence or 3’ ITR sequence comprises a modified ITR sequence containing one or more restriction enzyme half- sites. 6. The method of any one of claims 1 to 5, wherein the synthetic AAV genome comprises at least two att sites flanking a gene of interest. 7. The method of claim 6, wherein the at least two att sites comprise a Bxb1 phage integrase att site. 8. The method of any of the preceding claims, wherein the at least one restriction enzyme comprises AfeI or EcoRV. 9. The method of claim 2, wherein the DNA ligase is T4 DNA ligase. 10. The method of claim 2 or claim 9, wherein the DNA ligase is added to the solution at 25°C for about 1.5 hours. 11. The method of claim 3, wherein a T5 exonuclease is added to the solution at 37°C for about 1 hour. 12. A composition comprising a synthetic AAV genome, wherein the synthetic AAV genome comprises a 5’ inverted terminal repeat (ITR) sequence, a truncated 3’ ITR sequence, a 3’ ITR sequence, and a truncated 5’ ITR sequence. 13. The composition of claim 12, wherein the synthetic AAV genome comprises SEQ ID: 1 (Segment-I Left ITR) or SEQ ID: 2 (Segment-II Right). 14. The composition of claim 12 or 13, wherein the synthetic AAV genome comprises SEQ ID: 3 (Segment-I Right ITR (Truncated)) or SEQ ID: 4 (Segment-II Right ITR (Truncated)).

15. The composition of claim 12, wherein the synthetic AAV genome comprises at least two att sites flanking a gene of interest. 16. A pharmaceutical formulation comprising the composition of any one of claims 12 to 15, further comprising one or more pharmaceutically acceptable carriers, buffers, diluents or excipients. 17. A nucleic acid segment that encodes a synthetic AAV genome, comprising a nucleotide sequence as set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:3, or SEQ ID NO: 4. 18. A method of delivering a synthetic AAV genome to a cell, comprising incorporating a synthetic AAV genome of any one of claims 13 to 16 into a delivery system or a pharmaceutical formulation of claim 17 into a delivery system. 19. The method of claim 18, wherein the delivery system is a liposome, a nanoparticle system, a peptide, an antibody, or an antibody subunit. 20. A method of treating a disease or condition in a subject, comprising administering to the subject a therapeutically effective amount of a synthetic AAV genome composition of claim 12. 21. The method of claim 20, wherein the synthetic AAV genome is incorporated into a delivery system. 22. The method of claim 20 or claim 21, wherein the disease or condition is related to a point mutation, an indel, or a gene deficiency in the subject.

Description:
VGENX.004WO PATENT SYNTHETIC AAV GENOMES FOR IMPROVED GENE DELIVERY CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims priority to U.S. Provisional Application No. 63/343,287, filed on May 18, 2022, which is hereby incorporated by reference in its entirety. Field of the Disclosure [0002] The present disclosure relates to the fields of biochemistry and medicine. More particularly, the present disclosure relates methods and compositions pertaining to synthetic AAV genomes. REFERENCE TO SEQUENCE LISTING [0003] The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled SeqListingVGENX004WO.xml, created April 11, 2023, which is approximately 4.6 kb in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety. BACKGROUND [0004] Recombinant adeno-associated viral (AAV) vectors are commonly used in human gene therapy. AAV vectors are attractive because they do not integrate into genomic DNA but transduce a wide variety of tissues where they establish as stable episomes that express transgenes indefinitely in terminally differentiated cells. However, known AAV vectors have significant constraints that limit their use in human gene therapy. For example, they may be limited by their payload size, pre-existing immunity, induced immunogenicity, purity, potency, or cost. SUMMARY [0005] The present disclosure provides a method for producing synthetic adeno- associated viral (AAV) genomes which can carry large payloads for improved gene delivery. In some embodiments, the method for producing synthetic adeno-associated viral (AAV) genomes for improved gene delivery includes cloning an expression cassette into a first AAV plasmid and into a second AAV plasmid. In some embodiments, the first AAV plasmid includes a 5’ inverted terminal repeat (ITR) sequence and a truncated 3’ ITR sequence. In some embodiments, the second AAV plasmid includes a 3’ inverted terminal repeat (ITR) sequence and a truncated 5’ ITR sequence. [0006] In some embodiments, the method includes contacting the first AAV plasmid and the second AAV plasmid with at least one restriction enzyme. In some embodiments, the method includes heating a solution including the first AAV plasmid and the second AAV plasmid, thereby providing a first DNA segment with a single-stranded DNA overhang portion from the first plasmid and a second DNA segment with a complementary single-stranded DNA overhang portion from the second plasmid. In some embodiments, the first DNA segment further includes a 5’ inverted terminal repeat (ITR) sequence and the single- stranded DNA overhang portion of the first DNA segment includes a truncated 3’ ITR sequence. In some embodiments, the second DNA segment further includes a 3’ inverted terminal repeat (ITR) sequence and the single-stranded DNA overhang portion includes a truncated 5’ ITR sequence. [0007] In some embodiments, the method includes cooling the solution so that the single-stranded DNA overhang portion of the first DNA segment hybridizes with the complementary single-stranded DNA overhang portion of the second DNA segment to form a synthetic AAV genome. [0008] In some embodiments, the method further includes adding a DNA ligase to the solution. In some embodiments, the DNA ligase is T4 DNA ligase. In some embodiments, the DNA ligase is added to the solution at 25°C for about 1.5 hours. In some embodiments, the method further includes adding an exonuclease to the solution. In some embodiments, a T5 exonuclease is added to the solution at 37°C for about 1 hour. In some embodiments, the method further includes applying the solution to a DNA purification column; and eluting the synthetic AAV genome. [0009] In some embodiments, the 5’ ITR sequence or 3’ ITR sequence includes a modified ITR sequence containing one or more restriction enzyme half-sites. In some embodiments, the synthetic AAV genome includes at least two att sites flanking a gene of interest. In some embodiments, the at least two att sites include a Bxb1 phage integrase att site. In some embodiments, the at least one restriction enzyme includes AfeI or EcoRV. [0010] In a further aspect, described herein is a composition including a synthetic AAV genome. In some embodiments, the synthetic AAV genome includes a 5’ ITR sequence, a truncated 3’ ITR sequence, a 3’ ITR sequence, and a truncated 5’ ITR sequence. [0011] In some embodiments, the synthetic AAV genome includes SEQ ID: 1 (Segment-I Left ITR) or SEQ ID: 2 (Segment-II Right). In some embodiments, the synthetic AAV genome includes SEQ ID: 3 (Segment-I Right ITR (Truncated)) or SEQ ID: 4 (Segment- II Right ITR (Truncated)). In some embodiments, the synthetic AAV genome includes at least two att sites flanking a gene of interest. [0012] In a further aspect, described herein is a pharmaceutical formulation including a composition as described herein, and further including one or more pharmaceutically acceptable carriers, buffers, diluents or excipients. [0013] In a further aspect, described herein is a nucleic acid segment that encodes a synthetic AAV genome. In some embodiments, the nucleic acid segment includes a nucleotide sequence as set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:3, or SEQ ID NO: 4. [0014] In a further aspect, described herein is a method of delivering a synthetic AAV genome to a cell. In some embodiments, the method includes incorporating a synthetic AAV genome as described herein into a delivery system, or a pharmaceutical formulation as described herein into a delivery system. In some embodiments, the delivery system is a liposome, a nanoparticle system, a peptide, an antibody, or an antibody subunit. [0015] In a further aspect, described herein are methods of treating a disease or condition in a subject. In some embodiments, the method includes administering to the subject a therapeutically effective amount of a synthetic AAV genome. In some embodiments, the synthetic AAV genome is incorporated into a delivery system. In some embodiments, the disease or condition is related to a point mutation, an indel, or a gene deficiency in the subject. BRIEF DESCRIPTION OF THE DRAWINGS [0016] In addition to the features described herein, additional features and variations will be readily apparent from the following descriptions of the drawings and exemplary embodiments. It is to be understood that these drawings depict typical embodiments, and are not intended to be limiting in scope. [0017] FIG. 1A illustrates a first step in a method of an embodiment of the disclosure; FIG. 1B illustrates a second step of an embodiment of the disclosure; FIG. 1C illustrates a third step of an embodiment of the disclosure; FIG. 1D illustrates a fourth step of an embodiment of the disclosure. [0018] FIG.2 is an image of a gel electrophoresis experiment illustrating the final size of a synthetic AAV genome of an embodiment of the disclosure. [0019] FIG.3 is an image of a GFP expression time course in HeLa cells. [0020] FIG. 4 illustrates the structure of modified left AAV2 (adeno-associated virus type 2) ITR according to SEQ ID NO: 1 of an embodiment of the disclosure. [0021] FIG. 5A illustrates the structure of a synthetic AAV including an ABCA4 expression cassette. [0022] FIG.5B is an image of a gel electrophoresis experiment illustrating the final size of a synthetic AAV genome of an embodiment of the disclosure. [0023] FIG.6 is an image of a GFP expression time course in HepG2 cells. [0024] FIG. 7A is an image of a graph depicting a reduction in target gene expression in HeLa cells relative to a no inhibitor group. [0025] FIG. 7B illustrates a method of modulating synthetic AAV expression, of an embodiment of the disclosure. [0026] FIG.8A illustrates a method of gene therapy correcting a point mutation via homologous recombination with a synthetic AAV genome. [0027] FIG. 8B illustrates a method of gene therapy correcting an indel via homologous recombination with a synthetic AAV genome. [0028] FIG. 8C illustrates a method of gene therapy including gene addition via homologous recombination with a synthetic AAV genome. [0029] FIG.8D illustrates a method of gene therapy correcting a point mutation via homologous recombination with a synthetic AAV genome with the addition of a nuclease. DETAILED DESCRIPTION [0030] The present disclosure provides compositions and methods for producing synthetic AAV genomes that are able to carry relatively large payloads and transfect target cells. For example, some of the synthetic AAV genomes described herein do not have a payload size limitation and are able to accommodate expression cassettes of almost any size (including large or small). For example, the payload size may be above about 5 kb. In other aspects, the synthetic AAV genomes may not include a capsid protein. The disclosed synthetic AAV genomes described herein which do not have capsid proteins or other protein components may be less likely to induce an undesirable immune response when administered in subjects. In further aspects of the disclosure, the methods of producing synthetic AAV genomes may not include viral processing, therefore the purification process of synthetic AAV genomes may be more efficient and yield AAV genome products with greater purity, as there are no empty capsid products. Additionally, the disclosed methods of producing synthetic AAV genomes may be completed in a single day. The present disclosure also relates to methods of treatment including administering a synthetic AAV genome as described herein to treat a variety of conditions. Definitions [0031] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which this disclosure belongs. All patents, applications, published applications, and other publications are incorporated by reference in their entirety. In the event that there is a plurality of definitions for a term herein, those in this section prevail unless stated otherwise. [0032] The articles “a” and “an” are used herein to refer to one or to more than one (for example, to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element. [0033] By “about” is meant a quantity, level, value, number, frequency, percentage, dimension, size, amount, temperature, weight or length that varies by as much as 30, 25, 20, 15, 10, 9, 8, 7,6, 5, 4, 3, 2 or 1% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, temperature, weight or length. [0034] Throughout this specification, unless the context requires otherwise, the words “comprise,” “comprises,” and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements. [0035] By “consisting of” is meant including, and limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of” indicates that the listed elements are required or mandatory, and that no other elements may be present. By “consisting essentially of” is meant including any elements listed after the phrase, and limited to other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they materially affect the activity or action of the listed elements. [0036] In some embodiments, the “purity” of any given agent (for example, antibody, polypeptide binding agent) in a composition may be specifically defined. For embodiments, certain compositions may comprise an agent that is at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% pure, including all decimals in between, as measured, for example and by no means limiting, by high pressure liquid chromatography (HPLC), a well- known form of column chromatography used frequently in biochemistry and analytical chemistry to separate, identify, and quantify compounds. [0037] As used herein, the term “isolated” is meant material that is substantially or essentially free from components that normally accompany it in its native state. For example, an “isolated cell” or “isolated population of cells” as used herein, includes a cell or population of cells that has been purified from sample material, including other cells, debris, or extraneous sample material from its naturally-occurring state, Alternatively, an “isolated cell” or “isolated population of cells” and the like, as used herein, includes the in vitro, extracorporeal, or other isolation and/or purification of a cell or population of cells from its natural environment, and from association with other components of the sample or material in which it occurs. In some embodiments, isolated means that the component is not significantly associated with in vivo substances. [0038] As used herein, “subject” refers to a human or a non-human mammal, for example, a dog, a cat, a mouse, a rat, a cow, a sheep, a pig, a goat, a non-human primate or a bird, for example, a chicken, as well as any other vertebrate or invertebrate. [0039] As used herein, “mammal” refers to its usual biological sense. Thus, it specifically includes, but is not limited to, primates, including simians (chimpanzees, apes, monkeys) and humans, cattle, horses, sheep, goats, swine, rabbits, dogs, cats, rodents, rats, mice, guinea pigs, or the like. [0040] An “effective amount” or a “therapeutically effective amount” as used herein refers to an amount of a therapeutic agent that is effective to relieve, to some extent, or to reduce the likelihood of onset of, one or more of the symptoms of a disease or condition, and includes curing a disease or condition. “Curing” means that the symptoms of a disease or condition are eliminated; however, certain long-term or permanent effects may exist even after a cure is obtained (such as extensive tissue damage). [0041] As used herein, the terms “treat,” “treatment,” or “treating” refers to administering a compound or pharmaceutical formulation to a subject for prophylactic and/or therapeutic purposes. The term “prophylactic treatment” refers to treating a subject who does not yet exhibit symptoms of a disease or condition, but who is susceptible to, or otherwise at risk of, a particular disease or condition, whereby the treatment reduces the likelihood that the patient will develop the disease or condition. The term “therapeutic treatment” also refers to administering treatment to a subject already suffering from a disease or condition. [0042] As used herein, the terms “administration” or “administering” refers to routes of introducing a compound or composition provided herein to an individual to perform its intended function. For example, “administration” means both intravitreal injection and injection via non intra-vitreal routes. Non-intravitreal routes can include subconjunctiva injection, sub-retinal injection, sub-tenon injection, retrobulbar injection and suprachoroidal injection. Additional examples also include gene therapy delivery with or without a delivery device. Other non-intravitreal routes include topical application to the eye and injections at other regions of the body intravenous and subcutaneous injection. [0043] As used herein, the term “co-administration” and similar terms are broad terms, and are to be given their ordinary and customary meaning to a person of ordinary skill in the art (and are not to be limited to a special or customized meaning), and refer without limitation to administration of the selected therapeutic agents to a single patient, and are intended to include treatment regimens in which the agents are administered by the same or different route of administration or at the same or different time. In some embodiments, the compounds disclosed herein are co-administered. [0044] As used herein, the term “pharmaceutical formulation” refers to a bio- compatible aqueous or non-aqueous solution, suspension, dispersion or other physical form that includes an optimized synthetic AAV genome wherein the synthetic AAV genome sequence is at a concentration suitable for administering an effective amount to a mammalian subject. [0045] As used herein, the term “carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutically active substances is well known in the art. Supplementary active ingredients can also be incorporated into the compositions. The phrase “pharmaceutically-acceptable” refers to molecular entities and compositions that do not produce a toxic, an allergic, or similar untoward reaction when administered to a host. [0046] As used herein, the terms “synthetic AAV genome” and “synthetic production of AAV genome” refers to an AAV genome and synthetic production methods thereof in an entirely cell-free environment. The production may involve one or more molecules in a manner that does not involve replication or other multiplication of the molecule by or inside of a cell or using a cellular extract. Synthetic production avoids contamination of the produced molecule with cellular contaminants, for example, cellular proteins or cellular nucleic acid, viral protein or DNA, insect protein or DNA and further avoids unwanted cellular-specific modification of the molecule during the production process, for example, methylation or glycosylation or other post-translational modification. [0047] As used herein, the terms “gap” and “nick” are used interchangeably and refer to a discontinued portion of synthetic DNA genome of the present disclosure, creating a stretch of single-stranded DNA portion in otherwise double-stranded DNA portion where there is no phosphodiester bond between adjacent nucleotides of one strand typically through damage or enzyme action. It is understood that one or more gaps or nicks allow for the release of torsion in the strand during DNA replication and that gaps or nicks are also thought to play a role in facilitating binding of transcriptional machinery. [0048] As used herein, the term “restriction enzyme” generally refers to an enzyme (for example, restriction endonuclease, etc.) that cuts DNA at sites within the DNA molecule. Restriction enzymes used herein may be specific to a recognition site and may fragment the nucleic acid molecules at a location at or in proximity to the restriction site. Restriction enzymes used may be naturally occurring enzymes or they may be modified. The restriction enzymes may be modified to detect a specific restriction site or a nucleotide analog. Alternatively or in addition, the restriction enzyme used may naturally be specific for a nucleotide analog and may fragment the nucleic acid molecules at a location or in proximity to the restriction site or nucleotide analog. In some cases, the restriction enzymes used are modification dependent restriction enzymes. In such examples, the restriction enzymes may specifically fragment the nucleic acid molecules only in the presence of a nucleotide analog and may not be able to fragment nucleic acid molecules in the absence of a nucleotide analog. [0049] As used herein, the term “DNA ligase,” as used herein, refers to a family of enzymes which catalyze the formation of a covalent phosphodiester bond between two distinct DNA strands, i.e. a ligation reaction. Two prokaryotic DNA ligases, namely the ATP- dependent T4 DNA ligase (isolated from the T4 phage), and the NAD+-dependent DNA ligase from E. coli, have become indispensable tools in molecular biology applications. Both enzymes catalyze the synthesis of a phosphodiester bond between the 3ƍ-hydroxyl group of one polynucleic acid, and the 5ƍ-phosphoryl group, of a second polynucleic acid, for instance at a nick between the two strands which are both hybridized to a third DNA strand. The mechanism of the ligation reaction catalyzed by this family of enzymes typically requires three enzymatic steps. The initial step involves attack of the Į-phosphoryl group of either ATP or NAD+, resulting in formation of a ligase-adenylate intermediate (AMP is covalently linked to a lysine residue of the enzyme), and concurrent release of either pyrophosphate (PPi) or nicotinamide mononucleotide (NAD+). In the second step of the enzymatic reaction, AMP is transferred to the 5ƍ end of the free 5ƍ phosphate terminus of one DNA strand, to form an intermediate species of DNA-adenylate. In the final step, ligase catalyzes the attack of the DNA-adenylate intermediate species by the 3ƍ hydroxyl group of the second DNA strand, resulting in formation of a phosphodiester bond and sealing of the nick between the two DNA strands, and concurrent release of AMP. [0050] As used herein, the term “terminal repeat” or “TR” includes any viral or non-viral terminal repeat or synthetic sequence that comprises at least one minimal required origin of replication and a region comprising a palindromic hairpin structure. A Rep-binding sequence (“RBS” or also referred to as Rep-binding element (RBE)) and a terminal resolution site (“TRS”) together constitute a “minimal required origin of replication” and thus the TR comprises at least one RBS and at least one TRS. TRs that are the inverse complement of one another within a given stretch of polynucleotide sequence are typically each referred to as an “inverted terminal repeat” or “ITR”. In the context of a virus, ITRs plays a critical role in mediating replication, viral particle and DNA packaging, DNA integration and genome and provirus rescue. TRs that are not inverse complement (palindromic) across their full length can still perform the traditional functions of ITRs, and thus, the term ITR is used to refer to a TR in an AAV genome that is capable of mediating replication of in the host cell. It will be understood by one of ordinary skill in the art that in a complex synthetic AAV genome configurations more than two ITRs or asymmetric ITR pairs may be present. [0051] The “ITR” can be artificially synthesized using a set of oligonucleotides comprising one or more desirable functional sequences (for example, palindromic sequence, RBS). The ITR sequence can be an artificial AAV ITR, an artificial non-AAV ITR, or an ITR physically derived from a viral AAV ITR (for example, ITR fragments removed from a viral genome). For example, the ITR can be derived from the family Parvoviridae, which encompasses parvoviruses and dependo viruses (for example, canine parvovirus, bovine parvovirus, mouse parvovirus, porcine parvovirus, human parvovirus B-19), or the SV40 hairpin that serves as the origin of SV40 replication can be used as an ITR, which can further be modified by truncation, substitution, deletion, insertion and/or addition. Parvoviridae family viruses consist of two subfamilies: Parvovirinae, which infect vertebrates, and Densovirinae, which infect invertebrates. Dependoparvo viruses include the viral family of the adeno- associated viruses (AAV) which are capable of replication in vertebrate hosts including, but not limited to, human, primate, bovine, canine, equine and ovine species. Typically, ITR sequences can be derived not only from AAV, but also from Parvovirus, lentivirus, goose virus, B19, in the configurations of wildtype, “doggy bone” and “dumbbell shape”, symmetrical or even asymmetrical ITR orientation. Although the ITRs are typically present in both 5’ and 3’ ends of an AAV vector, ITR can be present in only one of end of the linear vector. For example, the ITR can be present on the 5’ end only. Some other cases, the ITR can be present on the 3’ end only in synthetic AAV genome. For convenience herein, an ITR located 5’ to (“upstream of’) an expression cassette in a synthetic AAV genome is referred to as a “5’ ITR” or a “left ITR”, and an ITR located 3’ to (“downstream of’) an expression cassette in a synthetic AAV genome is referred to as a “3’ ITR” or a “right ITR”. [0052] As used herein, the term “flanking” refers to a relative position of one nucleic acid sequence with respect to another nucleic acid sequence. Generally, in the sequence ABC, B is flanked by A and C. The same is true for the arrangement AxBxC. Thus, a flanking sequence precedes or follows a flanked sequence but need not be contiguous with, or immediately adjacent to the flanked sequence. [0053] As used herein, the terms “sense” and “antisense” refer to the orientation of the structural element on the polynucleotide. The sense and antisense versions of an element are the reverse complement of each other. [0054] As used herein, the term “promoter” refers to any nucleic acid sequence that regulates the expression of another nucleic acid sequence by driving transcription of the nucleic acid sequence, which can be a heterologous target gene encoding a protein or an RNA. Promoters can be constitutive, inducible, repressible, tissue-specific, or any combination thereof. A promoter is a control region of a nucleic acid sequence at which initiation and rate of transcription of the remainder of a nucleic acid sequence are controlled. A promoter can also contain genetic elements at which regulatory proteins and molecules can bind, such as RNA polymerase and other transcription factors. Within the promoter sequence will be found a transcription initiation site, as well as protein binding domains responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Various promoters, including inducible promoters, may be used to drive the expression of transgenes in the synthetic AAV vectors disclosed herein. A promoter sequence may be bounded at its 3’ terminus by the transcription initiation site and extends upstream (5’ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. [0055] As used herein, the terms “expression cassette” and “expression unit” are used interchangeably and refer to a heterologous DNA sequence that may be operably linked to a promoter or other DNA regulatory sequence sufficient to direct transcription of a transgene of a DNA vector, for example, synthetic AAV genome. [0056] As used herein, “operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. A promoter can be said to drive expression or drive transcription of the nucleic acid sequence that it regulates. The phrases “operably linked,” “operatively positioned,” “operatively linked,” “under control,” and “under transcriptional control” indicate that a promoter is in a correct functional location and/or orientation in relation to a nucleic acid sequence it regulates to control transcriptional initiation and/or expression of that sequence. An “inverted promoter,” as used herein, refers to a promoter in which the nucleic acid sequence is in the reverse orientation, such that what was the coding strand is now the non-coding strand, and vice versa. Inverted promoter sequences can be used in various embodiments to regulate the state of a switch. In addition, in various embodiments, a promoter can be used in conjunction with an enhancer. [0057] As used herein, the term “exogenous” refers to a substance present in a cell other than its native source. The term “exogenous” when used herein can refer to a nucleic acid (for example, a nucleic acid encoding a polypeptide) or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is not normally found and one wishes to introduce the nucleic acid or polypeptide into such a cell or organism. Alternatively, “exogenous” can refer to a nucleic acid or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is found in relatively low amounts and one wishes to increase the amount of the nucleic acid or polypeptide in the cell or organism, for example, to create ectopic expression or levels. In contrast, the term “endogenous” refers to a substance that is native to the biological system or cell. [0058] As used herein, the terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, this term includes single, double, or multi- stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer including purine and pyrimidine bases or other natural, chemically or biochemically modified, non- natural, or derivatized nucleotide bases. “Oligonucleotide” generally refers to polynucleotides of between about 5 and about 100 nucleotides of single- or double -stranded DNA. However, for the purposes of this disclosure, there is no upper limit to the length of an oligonucleotide. Oligonucleotides are also known as “oligomers” or “oligos” and may be isolated from genes, or chemically synthesized by methods known in the art. The terms “polynucleotide” and “nucleic acid” should be understood to include, as applicable to the embodiments being described, single-stranded (such as sense or antisense) and double-stranded polynucleotides. DNA may be in the form of, for example, antisense molecules, plasmid DNA, DNA-DNA duplexes, pre-condensed DNA, PCR products, vectors (PI, PAC, BAC, YAC, artificial chromosomes), expression cassettes, chimeric sequences, chromosomal DNA, or derivatives and combinations of these groups. DNA may be in the form of minicircle, plasmid, bacmid, minigene, ministring DNA (linear covalently closed DNA vector), closed-ended linear duplex DNA (CELiD or ceDNA), doggybone (dbDNA™) DNA, dumbbell shaped DNA, minimalistic immunological-defined gene expression (MIDGE) -vector, viral vector or nonviral vectors. RNA may be in the form of small interfering RNA (siRNA), Dicer- substrate dsRNA, small hairpin RNA (shRNA), asymmetrical interfering RNA (aiRNA), microRNA (miRNA), mRNA, rRNA, tRNA, viral RNA (vRNA), and combinations thereof. Nucleic acids include nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, and which have similar binding properties as the reference nucleic acid. Examples of such analogs and/or modified residues include, without limitation, phosphorothioates, phosphorodiamidate morpholino oligomer (morpholino), phosphoramidates, methyl phosphonates, chiral -methyl phosphonates, 2’-O-methyl ribonucleotides, locked nucleic acid (LNA™), and peptide nucleic acids (PNAs). Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (for example, degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated. “Nucleotides” contain a sugar deoxyribose (DNA) or ribose (RNA), a base, and a phosphate group. Nucleotides are linked together through the phosphate groups. [0059] As used herein, the term “bases” include purines and pyrimidines, which further include natural compounds adenine, thymine, guanine, cytosine, uracil, inosine, and natural analogs, and synthetic derivatives of purines and pyrimidines, which include, but are not limited to, modifications which place new reactive groups such as, but not limited to, amines, alcohols, thiols, carboxylates, and alkylhalides. [0060] As used herein, the terms “hybridizable” or “complementary” or “substantially complementary” refers to a nucleic acid (for example, RNA) including a sequence of nucleotides that enables it to non-covalently bind, i.e. form Watson-Crick base pairs and/or G/U base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence- specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and/or in vivo conditions of temperature and solution ionic strength. As is known in the art, standard Watson-Crick base-pairing includes: adenine (A) pairing with thymidine (T), adenine (A) pairing with uracil (U), and guanine (G) pairing with cytosine (C). In addition, it is also known in the art that for hybridization between two RNA molecules (for example, dsRNA), guanine (G) base pairs with uracil (U). For example, G/U base-pairing is partially responsible for the degeneracy (i.e., redundancy) of the genetic code in the context of tRNA anti -codon base-pairing with codons in mRNA. In the context of this disclosure, a guanine (G) of a protein-binding segment (dsRNA duplex) of a subject DNA- targeting RNA molecule is considered complementary to a uracil (U), and vice versa. As such, when a G/U base-pair can be made at a given nucleotide position a protein-binding segment (dsRNA duplex) of a subject DNA-targeting RNA molecule, the position is not considered to be non-complementary, but is instead considered to be complementary. [0061] As used herein, the term “recombinant” refers to nucleic acids, vectors, polypeptides, or proteins that have been generated using DNA recombination (cloning) methods and are distinguishable from native or wild-type nucleic acids, vectors, polypeptides, or proteins. [0062] As used herein, the term “adeno-associated virus” (AAV), includes but is not limited to, AAV serotype 1, AAV serotype 2, AAV serotype 3 (including serotypes 3A and 3B), AAV serotype 4, AAV serotype 5, AAV serotype 6, AAV serotype 7, AAV serotype 8, AAV serotype 9, AAV serotype 10, AAV serotype 11, AAV serotype 12, AAV serotype 13, snake AAV, avian AAV, bovine AAV, canine AAV, equine AAV, ovine AAV, goat AAV, shrimp AAV, and any other AAV now known or later discovered. [0063] As used herein, an “AAV genome” refers to a genome derived from an adeno-associated virus serotype, including without limitation, AAV-1, AAV-2, AAV-3, AAV- 4, AAV-5, AAV-6, AAV-7 and AAV-8. AAV genome can have one or more of the AAV wild- type genes deleted in whole or part, preferably the rep and/or cap genes, but retain functional flanking ITR sequences. Functional ITR sequences are necessary for the rescue, replication and packaging of the AAV virion. Thus, an AAV genome is defined herein to include at least those sequences required in cis for replication and packaging (for example, functional ITRs) of the virus. The ITRs need not be the wild-type nucleotide sequences, and may be altered, for example, by the insertion, deletion or substitution of nucleotides, so long as the sequences provide for functional rescue, replication and packaging. [0064] As used herein, “AAV inverted terminal repeat” or “AAV ITR” refers to any AAV, including but not limited to serotypes 1, 2, 3a, 3b, 4, 5, 6, 7, 8, 9, 10, 11, or 13, snake AAV, avian AAV, bovine AAV, canine AAV, equine AAV, ovine AAV, goat AAV, shrimp AAV, or any other AAV now known or later discovered with one or more inverted terminal repeat sequence. An AAV ITR need not have the native terminal repeat sequence (for example, a native AAV ITR sequence may be altered by insertion, deletion, truncation and/or missense mutations), as long as the terminal repeat mediates the desired functions, for example, replication, virus packaging, integration, and/or provirus rescue, and the like. [0065] As used herein, “AAV virion” refers to a virus particle, such as a wild-type (wt) AAV virus particle (comprising a linear, single-stranded AAV nucleic acid genome associated with an AAV capsid protein coat). In this regard, single-stranded AAV nucleic acid molecules of either complementary sense, for example, “sense” or “antisense” strands, can be packaged into any one AAV virion and both strands are equally infectious. [0066] As used herein, the term “expression” refers to the cellular processes involved in producing RNA and proteins and as appropriate, secreting proteins, including where applicable, but not limited to, for example, transcription, transcript processing, translation and protein folding, modification and processing. [0067] As used herein, the phrase “expression products” include RNA transcribed from a gene (for example, transgene), and polypeptides obtained by translation of mRNA transcribed from a gene. [0068] As used herein, the term “gene” means the nucleic acid sequence which is transcribed (DNA) to RNA in vitro or in vivo when operably linked to appropriate regulatory sequences. The gene may or may not include regions preceding and following the coding region, for example, 5’ untranslated region (5’ UTR) or “leader” sequences and 3’ UTR or “trailer” sequences, as well as intervening sequences (introns) between individual coding segments (exons). [0069] As used herein, “genetic disease” refers to a disease, partially or completely, directly or indirectly, caused by one or more abnormalities in the genome, especially a condition that is present from birth and can be treated by a synthetic AAV vector described herein. The abnormality may be a mutation, an insertion or a deletion. The abnormality may affect the coding sequence of the gene or its regulatory sequence. The genetic disease may be, but not limited to phenylketonuria (PKU), sickle-cell anemia, melanoma, hemophilia A (clotting factor VIII (FVIII) deficiency) and hemophilia B (clotting factor IX (FIX) deficiency), cystic fibrosis, Huntington’s chorea, familial hypercholesterolemia (LDL receptor defect), hepatoblastoma, Wilson’s disease, congenital hepatic porphyria, inherited disorders of hepatic metabolism, Lesch Nyhan syndrome, sickle cell anemia, thalassaemias, xeroderma pigmentosum, Fanconi’s anemia, retinitis pigmentosa, ataxia telangiectasia, Bloom’s syndrome, retinoblastoma, and mucopolysaccharide storage diseases (for example, Hurler syndrome (MPS Type I), Scheie syndrome (MPS Type I S), Hurler-Scheie syndrome (MPS Type I H-S), Hunter syndrome (MPS Type II), Sanfilippo Types A, B, C, and D (MPS Types III A, B, C, and D), Morquio Types A and B (MPS IVA and MPS IVB), Maroteaux-Lamy syndrome (MPS Type VI), Sly syndrome (MPS Type VII), hyaluronidase deficiency (MPS Type IX)), Niemann-Pick Disease Types A/B, Cl and C2, Fabry disease, Schindler disease, GM2 -gangliosidosis Type II (Sandhoff Disease), Tay-Sachs disease, Metachromatic Leukodystrophy, Krabbe disease, Mucolipidosis Type I, II/III and IV, Sialidosis Types I and II, Glycogen Storage disease Types I and II (Pompe disease), Gaucher disease Types I, II and III, Fabry disease, cystinosis, Batten disease, Aspartylglucosaminuria, Salla disease, Danon disease (LAMP-2 deficiency), Lysosomal Acid Lipase (LAL) deficiency, neuronal ceroid lipofuscinoses (CLNl-8, INCL, and LINCL), sphingolipidoses, galactosialidosis. Also included in genetic disorders are amyotrophic lateral sclerosis (ALS), Parkinson’s disease, Alzheimer’s disease, Huntington’s disease, spinocerebellar ataxia, spinal muscular atrophy, Friedreich’s ataxia, Duchenne muscular dystrophy (DMD), Becker muscular dystrophies (BMD), dystrophic epidermolysis bullosa (DEB), ectonucleotide pyrophosphatase 1 deficiency, generalized arterial calcification of infancy (GACI), Leber Congenital Amaurosis (LCA, for example, LCA10 [CEP290]), Stargardt macular dystrophy (ABCA4), or Cathepsin A deficiency. [0070] As used herein, “modified ITR sequence” or “modified inverted terminal repeat sequence” refers to an ITR sequence modified to comprise one or more restriction enzyme half-sites as further described herein. [0071] As used herein, “half-site” refers to a sequence comprising a portion (such as half) of a restriction enzyme cleavage site. For example, EcoRV has a cut site “GAT^ATC,” with the cut denoted by “^,” such that a half-site may be, for example, “GAT” or “ATC.” [0072] As used herein, “att site” refers to loci where phage enzymes attach (“att”) to a genome. A pair of att sites may comprise an attP and an attB site. A phage integrase may attach att sites to carry out recombination between att sites. As a result of recombination, an attL and an attR site may be produced. Methods of Making a Synthetic AAV Genome [0073] In some aspects, a method for producing synthetic adeno-associated viral (AAV) genomes for improved gene delivery is provided. In some embodiments, the method for producing synthetic AAV genomes is an in vitro process. [0074] In some embodiments, the method includes cloning an expression cassette into a first AAV plasmid and into a second AAV plasmid. In some embodiments, the first AAV plasmid includes a 5’ inverted terminal repeat (ITR) sequence and a truncated 3’ ITR sequence. In some embodiments, the second AAV plasmid includes a 3’ ITR sequence and a truncated 5’ ITR sequence. [0075] In some embodiments, the expression cassette may comprise any transgene useful for treating, ameliorating or preventing a disease or condition in a subject. In some embodiments, the expression cassette encodes a ELOVL2 transgene. In some embodiments, the expression cassette may comprise any transgene to upregulate the expression of one or more additional genes. In some embodiments, the expression cassette encodes ABCA4 (ATP binding cassette subfamily A member 4). In some embodiments, expression cassette encodes DMD (Duchenne Muscular Dystrophy) gene. The expression cassette may be cloned into the first AAV plasmid and/or second AAV plasmid using any method known to those of skill in the art. [0076] In some embodiments, the expression cassette may also encode polypeptides, sense or antisense oligonucleotides, or RNAs (coding or non-coding; for example, siRNAs, shRNAs, micro-RNAs, and their antisense counterparts (for example, antagoMiR)). In some embodiments, expression cassettes may include an exogenous sequence that encodes a reporter protein to be used for experimental or diagnostic purposes, such as b- lactamase, b -galactosidase (LacZ), alkaline phosphatase, thymidine kinase, green fluorescent protein (GFP), chloramphenicol acetyltransferase (CAT), luciferase, and others well known in the art. In some embodiments, the expression cassette is CMV-GFP. [0077] In some embodiments, the expression cassette may further include a promoter. In some embodiments, the promoter in the expression cassette is selected from SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6) (Miyagishi el al, Nature Biotechnology 20, 497- 500 (2002)), an enhanced U6 promoter (for example, Xia et al, Nucleic Acids Res. 2003 Sep. 1; 31(17)), a human HI promoter (HI), a CAG promoter, a human alpha 1-antitypsin (HAAT) promoter, elongation factor 1 -alpha (Efla) promoter, CB7 promoter, and the like. In some embodiments, the promoter may be of AAV origin. In some embodiments, the expression cassette does not include a promoter. In some embodiments, a promoter from a host cell may be used. For example, a gene of interest may be inserted in a host genome downstream of a host promoter through recombination. [0078] In some embodiments, the expression cassette includes wild-type genomic DNA flanking a gene of interest. In some embodiments, the expression cassette includes approximately 1,000 bp of genomic DNA flanking a gene of interest. In some embodiments, the expression cassette includes approximately 200 bp to 2,000 bp of genomic DNA flanking a gene of interest, or a value within the aforementioned range. [0079] In some embodiments, the first AAV plasmid includes a 5’ inverted terminal repeat (ITR) sequence and a truncated 3’ ITR sequence. In some embodiments, the second AAV plasmid further includes a 3’ inverted terminal repeat (ITR) sequence and a truncated 5’ ITR sequence. In some embodiments, the 5’ ITR sequence includes a 5’ modified ITR sequence which includes one or more restriction enzyme half-sites. In some embodiments, the 3’ ITR sequence includes a 3’ modified ITR sequence which includes one or more restriction enzyme half-sites. [0080] The following table discloses modified ITR sequences and truncated ITR sequences that may be used in some embodiments of the present disclosure. In Table 1, bold is used to show an EcoRV half-site, while italics are used to show an Afel half-site. Table 1 [0081] In some embodiments, the 5’ modified ITR sequence and/or the 3’ modified ITR sequence comprise one or more restriction enzyme half-sites. For example, the 5’ modified ITR sequence and/or the 3’ modified ITR sequence may comprise two adjacent restriction enzyme half-sites. The two adjacent restriction enzyme half-sites correspond to two different restriction enzymes with different cut sites. For example, the 5’ modified ITR sequence of SEQ ID NO: 1 comprises a first half-site comprising the first half of the EcoRV cut site (“GAT”) adjacent to a second half-site comprising the second half of the Afel cut site (“GCT”), and the 3’ modified ITR sequence of SEQ ID NO: 4 comprises a first half-site comprising the first half of the Afel cut site (“ACG”) adjacent to a second half-site comprising the second half of the EcoRV cut site (“ATC”). In some embodiments, and without being bound by theory, a half- site is included to anneal with an end cut by a restriction enzyme. [0082] In some embodiments, a truncated 5’ ITR sequence comprises a portion of the 5’ ITR sequence. For example, the truncated 5’ ITR sequence may comprise a portion comprising about 10 bases, about 20 bases, about 30 bases, about 40 bases, about 50 bases, about 60 bases, about 70 bases, or about 80 bases of the 5’ ITR sequence, or ranges including and/or spanning the aforementioned values. For example, the truncated 5’ ITR sequence may comprise a portion comprising about 40 to about 60 bases of the 5’ ITR sequence, for example, the first about 40 to about 60 bases. The truncated 5’ ITR sequence may comprise the first portion (using the 5’ to 3’ alignment) of the 5’ ITR sequence. For example, the truncated 5’ ITR sequence may comprise the first 54 bases of the 5’ ITR sequence. For example, in some embodiments, the 5’ ITR sequence has the sequence set forth in SEQ ID NO: 1, and the truncated 5’ ITR sequence has the sequence set forth in SEQ ID NO: 3. [0083] In some embodiments, a truncated 3’ITR sequence comprises a portion of the 3’ ITR sequence. For example, the truncated 3’ITR sequence may comprise a portion comprising about 10 bases, about 20 bases, about 30 bases, about 40 bases, about 50 bases, about 60 bases, about 70 bases, or about 80 bases of the 3’ ITR sequence, or ranges including and/or spanning the aforementioned values. For example, the truncated 3’ ITR sequence may comprise a portion comprising about 40 to about 60 bases of the 3’ ITR sequence. The truncated 3’ ITR sequence may comprise the first portion (using the 5’ to 3’ alignment) of the 3’ ITR sequence, for example the first about 40 to about 60 bases. For example, the truncated 3’ ITR sequence may comprise the first 54 bases of the 3’ ITR sequence. For example, in some embodiments, the 3’ ITR sequence has the sequence set forth in SEQ ID NO: 4, and the truncated 3’ ITR sequence has the sequence set forth in SEQ ID NO: 2. [0084] [0075] In some embodiments, the 5’ ITR sequence and/or the 3’ ITR sequence comprise an ITR sequence, for example as shown in SEQ ID NO: 1 and/or SEQ ID NO: 4. In some embodiments, the ITR sequence may be longer than the sequences provided in SEQ ID NO: 1 and SEQ ID NO: 4. For example, in some embodiments, the ITR sequence may comprise more extensive regions of self-complementary base pairs. In some embodiments, the ITR sequence comprising extensive regions of self-complementary base pairs provides increased synthetic genome stability. In some embodiments, the ITR sequence comprising extensive regions of self-complementary base pairs provides a longer lasting transgene expression. [0085] In some embodiments, the method includes mixing the first AAV plasmid and the second AAV plasmid in a solution. In some embodiments, the first AAV plasmid and the second AAV plasmid may be in a 1:1 ratio. In some embodiments, the first AAV plasmid and the second AAV plasmid are mixed in about a 1:1 ratio. In some embodiments, the first AAV plasmid and the second AAV plasmid are mixed in a ratio ranging from 2:1 to 1:2. [0086] In some embodiments, the method includes contacting the first AAV plasmid and the second AAV plasmid with at least one restriction enzyme. In some embodiments, the at least one restriction enzyme may be selected from AatII, AbaSI, Acc65I, AccI, AcdI, AciI, AclI, AcuI, AfeI, AflII, AflIII, AgeI, AhdI, AleI, AluI, AlwI, AlwNI, ApaI, ApaLI, ApeKI, ApoI, SoxI, AscI, AseI, AsiSI, AspBHI, AvaI, AvaII, AvrII, BaeGI, BaeI, BamHI, BanI, BanII, BbeI, BbsI, BbvCI, BbvI, BccI, BceAI, BcgI, BciVI, BclI, BcoDI, BfaI, BfuAI, BglI, BgII, BlpI, BisI, BmgBI, BmrI, BmtI, BpmI, Bpu10I, BpuEI, BsaAI, BsaBI, BsaHI, BsaI, BsaJI, BsaWI, BsaXI, BseRI, BseYI, BsgI, BsiEI, BsiHKAI, BsiWI, BslI, BsmAI, BsmBI, BsmFI, BsmI, BsoBI, Bsp1286I, BspCNI, BspDI, BspEI, BspHI, BspMI, BspQI, BsrBI, BsrDI, BsrFI, BsrGI, BsrI, BssHII, BssKI, BssS_I, BstAPI, BstBI, BstEII, BstNI, BstUI, BstXI, BstYI, Bsu36I, BtgI, BtgZI, BtsCI, BtsIMutI, Bts_I, Cac8I, ClaI, CspCI, CviAII, CviKIl, CviQI, DdeI, DpnI, DpnII, DraI, DrdI, EaeI, EagI, Earl, EciI, Eco53kI, EcoK, EcoNI, EcoO109I, EcoP15I, EcoRI, EcoRV, Esp3I, FatI, FauI, Fnu4HI, FokI, FseI, FspEI, FspI, Glal, GluI, HaeII, HaeIII, HgaI, HhaI, HincII, HindIII, Hinfi, HinPlI, HpaI, HpaII, HphI, Hpy166II, Hpy188I, Hpy188III, Hpy99I, HpyAV, HpyCH4III, HpyCH4IV, HpyCH4V, I- CeuI, I-SceI, KasI, KpnI, KroI, LpnI, LpnPI, MalI, MboI, MboII, McrA, McrBC, MfeI, MluCI, MluI, MlyI, MmeI, MnlI, MrrIA, MscI, MseI, MslI, MspAlI, MspI, MspJI, MteI, MwoI, NaeI, Narl, Nb.BbvCI, Nb.BsmI, Nb.BsrDI, Nb.BssSI, Nb.BtsI, NciI, NcoI, NdeI, NgoMIV, NheI, NlaIII, NlaIV, NmeAIII, NotI, NruI, NsiI, NspI, Nt.AlwI, Nt.BbvCI, Nt.BsmAI, Nt.BspQI, Nt.BstNBI, Nt.CviPII, PacI, PaeR7I, PciI, PsI, PflFI, PflMI, PkrI, PI-PspI, PI-SceI, PleI, PluTI, PmeI, PmlI, PpuMI, PshAI, PsiI, PspGI, PspOMI, PspXI, PstI, PvuI, PvuII, RlaI, RsaI, RsrII, SacI, SacII, SalI, SapI, Sau3AI, Sau96I, SauNewI, SauUSI, SbfI, ScoA3, ScrFI, SepR, SexAl, SfaNI, SfcI, SfiI, SfoI, SgeI, SgrAI, SmaI, SmlI, SnaBI, SpeI, SphI, Srfl, SspI, StuI, StyD4I, StyI, SwaI, Taq_I, TfiI, TseI, Tsp45I, TspMI, TspRI, Tth111I, XbaI, XcmI, XhoI, XmaI, XmnI, and ZmoMrr. In some embodiments, the at least one restriction enzyme includes one restriction enzyme. In some embodiments, the at least one restriction enzymes includes two or more different restriction enzymes. In some embodiments, the at least one restriction enzyme includes EcoRV or AfeI. In some embodiments, the at least one restriction enzyme includes EcoRV and AfeI. For example, in FIG. 1A, a first AAV plasmid and a second AAV plasmid are cut with restriction enzymes. [0087] In some embodiments, the restriction enzyme amount is about 10 units or about 1 μL. In some embodiments, the restriction enzyme amount is about 5 units, about 6 units, about 7 units, about 8 units, about 9 units, about 10 units, about 11 units, about 12 units, about 13 units, about 14 units, about 15 units, or ranges including and/or spanning the aforementioned values. In some embodiments, the restriction enzyme amount is about 0.1 μL, about 0.5 μL, about 1 μL, about 1.5 μL, about 2 μL, about 2.5 μL, or ranges including and/or spanning the aforementioned values. The amount of restriction enzyme may be readily determined by one of skill in the art based on the amount of first and second AAV plasmid to be used. [0088] In some embodiments, the method includes heating a solution comprising the first AAV plasmid and the second AAV plasmid, thereby providing a first DNA segment with a single-stranded DNA overhang portion from the first AAV plasmid and a second DNA segment with a complementary single-stranded DNA overhang portion from the second AAV plasmid. [0089] In some embodiments, the solution is heated to about 90°C, 91°C, 92°C, 93°C, 94°C, 95°C, 96°C, 97°C, 98°C, 99°C, 100°C or ranges including and/or spanning the aforementioned values. In some embodiments, the solution is heated to about 95°C for about 30 seconds, 35 seconds, 40 seconds, 45 seconds, 50 seconds, 55 seconds, 1 minute, 1 minute and 5 seconds, 1 minute and 10 seconds, 1 minute and 15 seconds, 1 minute and 20 seconds, 1 minute and 25 seconds, or 1 minute and 30 seconds. In some embodiments, the solution is heated to about 95°C for between 30 seconds to about 1 minute and 30 seconds, or ranges including and/or spanning the aforementioned values. In some embodiments, the solution is heated between 90°C and 100°C for about 30 seconds to about 1 minute and 30 seconds. In some embodiments, the method includes heating the solution up to about 95°C for about 1 minute. In some embodiments, heating the solution separates the DNA strands, thereby providing a first DNA segment corresponding to the first AAV plasmid and a second DNA segment corresponding to the second AAV plasmid. [0090] In some embodiments, the first DNA segment further comprises a 5’ inverted terminal repeat (ITR) sequence and the single-stranded DNA overhang portion of the first DNA segment comprises a truncated 3’ ITR sequence. In some embodiments, the second DNA segment further comprises a 3’ inverted terminal repeat (ITR) sequence and the single- stranded DNA overhang portion comprises a truncated 5’ ITR sequence. In some embodiments, a ITR sequence folds and hybridize to itself, for example, as depicted in FIG.4. [0091] For example, in the embodiment FIG. 1B, a first DNA segment comprises an expression cassette, a 5’ ITR sequence folded and hybridized to itself, and a single-stranded DNA overhang portion which comprises a truncated 3’ ITR sequence. Further, in the embodiment of FIG. 1B, a second DNA segment comprises a 3’ ITR sequence folded and hybridized to itself, and a single-stranded DNA overhang portion which comprises a truncated 5’ ITR sequence and which is complementary to the single-stranded DNA overhang portion of the first DNA segment. [0092] In some embodiments, the method includes cooling the solution. In some embodiments, cooling the solution may induce the single-stranded DNA overhang portion of the first DNA segment to hybridize with the complementary single-stranded DNA overhang portion of the second DNA segment to form a synthetic AAV genome. The methods of cooling a solution to allow hybridization of nucleic acids may be any method known to those of skill in the art. For example, in some embodiments, the solution is cooled slowly to room temperature (68 to 77°F (20 to 25°C)). [0093] In some embodiments, the synthetic AAV genome formed after cooling the solution includes with a first nick and a second nick. In some embodiments, the nick can be 1 base-pair to 100 base- pair long in length. Typical nicks, designed and created by the methods described herein and synthetic vectors generated by the methods can be, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59 or 60 base pairs (bp) long in length. Exemplified nicks in the present disclosure can be 1 bp to 10 bp long, 1 to 20 bp long, 1 to 30 bp long, or any length necessary to nick double stranded DNA to allow for or to maintain efficient transcription of an expression cassette in host cells. According to some embodiments, nicks can be present 5’ upstream of an expression cassette. According to some embodiments, nicks can be present 3’ downstream of an expression cassette. According to some embodiments, nicks can be present 5’ upstream of an expression cassette and 3’ downstream of an expression cassette. [0094] In some embodiments, the method further includes adding a DNA ligase to the solution. In some embodiments, adding a DNA ligase to the solution may remove the first nick and remove the second nick to form the synthetic AAV genome. In some embodiments, the DNA ligase may be selected from T4 DNA ligase, T3 DNA ligase, T7 DNA ligase, Taq DNA ligase, E. coli DNA ligase, ElectroLigase®, 9°N™ DNA ligase, and SplintR® ligase. In some embodiments, the DNA ligase is T4 DNA ligase. In some embodiments, the DNA ligase is about 1 μL. In some embodiments, DNA ligase is added to the solution at about 25°C for 1.5 hours. In some embodiments, DNA ligase is added to the solution at about 20°C, 21°C, 22°C, 23°C, 24°C, 25°C, 26°C, 27°C, 28°C, 29°C, or 30°C for 1.5 hours. In some embodiments, DNA ligase is added to the solution at 25°C for 1.25 hours, 1.3 hours, 1.35 hours, 1.4 hours, 1.45 hours, or 1.5 hours, 1.55 hours, 1.6 hours, 1.65 hours, 1.7 hours, or 1.75 hours. In some embodiments, DNA ligase is added to the solution at between 20°C – 30°C for about 1.25 hours –1.75 hours. [0095] In some embodiments, the method further includes adding an exonuclease to the solution. In some embodiments, the exonuclease is added before addition of a DNA ligase. In some embodiments, without being bound by theory, addition of the exonuclease improves exonuclease resistance of the synthetic AAV genome. [0096] In some embodiments, the exonuclease is added after addition of a DNA ligase. In some embodiments, and without being bound by theory, the exonuclease degrades any DNA in the solution that is not a double-stranded sealed circle. For example, in some embodiments, the exonuclease degrades the plasmid backbone left in the solution and/or degrades any mis-paired DNA fragments left in the solution. [0097] In some embodiments, a first exonuclease is added before addition of a DNA ligase, and a second exonuclease is added after addition of the DNA ligase. For example, in some embodiments, the synthetic AAV genome becomes resistant to the first exonuclease (for example, ExoV) because it is a closed-ended linear nicked molecule when exposed to the first exonuclease, and the AAV genome becomes resistant to the second exonuclease (such as T5) after the nicks are sealed by addition of a ligase (such as T4 ligase), the synthetic AAV genome becomes a closed ended linear molecule, and the synthetic AAV genome is treated with the second exonuclease, . [0098] In some embodiments, the exonuclease (such as the first or second exonuclease) is selected from Exonuclease III, T7 exonuclease, Exonuclease V, Exonuclease VIII, Lambda Exonuclease, or T5 exonuclease. In some embodiments, the exonuclease is T5 exonuclease. In some embodiments, the exonuclease is about 10 units or 1 μL. In some embodiments, the exonuclease is added at about 37°C for about 1 hour. In some embodiments, the exonuclease is added at about 33°C, 34°C, 35°C, 36°C, 37°C, 38°C, 39°C or 40°C for about 1 hour. In some embodiments, the exonuclease is added at about 33°C, 34°C, 35°C, 36°C, 37°C, 38°C, 39°C or 40°C for about 30 minutes, 40 minutes, 50 minutes, 1 hour, 1 hour and 10 minutes, 1 hour and 20 minutes, and 1 hour and 30 minutes. In some embodiments, exonuclease is added to the solution at between 33°C–40°C for about between 30 minutes and 1 hour and 30 minutes. In some embodiments, the exonuclease is added at about 37°C for about 30 minutes. [0099] In some embodiments, the method further includes concentrating an amount of the synthetic AAV genome. In some embodiments, the synthetic AAV genome is concentrated by application to a DNA purification column. In some embodiments, the DNA purification column is a spin column. In some embodiments, the spin column may comprises glass fiber, derivatized silica or an ion exchange membrane. In some embodiments, the synthetic AAV genome is concentrated using another method known to those of skill in the art. [0100] In some embodiments, the method includes eluting the synthetic AAV genome. In some embodiments, the synthetic AAV genome is eluted from a DNA purification column to provide a concentrated solution comprising the synthetic AAV genome. [0101] In some embodiments, the synthetic AAV genome comprises at least two att sites flanking a gene of interest. For example, the synthetic AAV genome may comprise an attP site upstream of a gene of interest, and an attB site downstream of a gene of interest. In some embodiments, after a cell is transfected with a synthetic AAV genome, the synthetic AAV genome within the cell may be contacted with a phage integrase. For example, the cell may be further transfected with a lipid nanoparticle containing an mRNA encoding a phage integrase. Without being bound by theory, as illustrated in FIG. 7B, in some embodiments, the phage integrase may carry out recombination between the at least two att sites such that the gene of interest is inverted, thus turning “off” expression of the gene of interest. Thus, in some embodiments, the synthetic AAV genome comprising at least two att sites provides for modulation of transgene expression levels. The at least two att sites may comprise att sites corresponding to any phage integrases known in the art. In some embodiments, the phage integrase is a tyrosine integrase or a serine integrase. In some embodiments, the at least two att sites comprise an att site corresponding to ^, Bxb1, ICEclc, L5, P2, P22, HP1, ijC31, ijRv1, ijBT1, ijFC1, R4, TG1, ^MR11, A118, or TP901-1 phage integrase. [0102] In some embodiments, the synthetic genome may be formulated as a composition for upregulating the expression of one or more additional genes. Methods of Treatment / Uses [0103] In some aspects, a method of treating, ameliorating or preventing a disease or condition in a subject is described herein. In some embodiments, the method comprises administering to the subject a therapeutically effective amount of a synthetic AAV genome. [0104] In some aspects, a method of delivering a synthetic AAV genome to a cell is described herein. In some embodiments, a synthetic AAV genome is incorporated into a delivery system. In some embodiments, a synthetic AAV genome is incorporated into a pharmaceutical formulation into a delivery system. [0105] In some embodiments, the delivery system is a liposome. In some embodiments, the delivery system is a nanoparticle system. In some embodiments, the delivery system is a lipid nanoparticle. In some embodiments, the delivery system is a peptide. In some embodiments, the delivery system is a peptide. In some embodiments, the delivery system is an antibody. In some embodiments, the delivery system is an antibody subunit. [0106] In some embodiments, the disease or condition is related to a point mutation, an indel, or a gene deficiency. In some embodiments, the subject’s DNA comprises a point mutation, an indel, or a gene deficiency. [0107] In some embodiments, the method further includes identifying a subject having a point mutation, an indel, or a gene deficiency. Such identification may be accomplished by, for example, sequencing the subject’s DNA, or based on phenotype (symptoms) associated with the point mutation, indel, or gene deficiency. [0108] In some embodiments, the disease or condition is a genetic disease. In some embodiments, the disease or condition is selected from the group consisting of proliferative diseases (cancers, tumors, dysplasias, etc.), Crigler-Najjar and metabolic diseases like metabolic diseases of the liver, Friedreich ataxia, infectious diseases, addiction (e.g., to tobacco, alcohol, or drugs), epilepsy, Canavan's disease, adrenoleukodystrophy, viral diseases (induced, e.g., by hepatitis B or C viruses, HIV, herpes, retroviruses, etc.), genetic diseases (cystic fibrosis, dystroglycanopathies, myopathies such as Duchenne muscular myopathy or dystrophy, myotubular myopathy, hemophilia A, hemophilia B, hemophilia A with inhibitors, hemophilia B with inhibitors, sickle-cell anemia, sickle cell disease, Fanconi's anemia, diabetes, amyotrophic lateral sclerosis (ALS), myotubularin myopathy, motor neuron diseases such as spinal muscular atrophy (SMA), spinobulbar muscular atrophy, or Charcot-Marie- Tooth disease, arthritis, severe combined immunodeficiencies (such as RS-SCID, ADA-SCID or X-SCID), Wiskott-Aldrich syndrome, X-linked thrombocytopenia, X-linked congenital neutropenia, chronic granulomatous disease, etc.), clotting factor deficiencies, cardiovascular disease (restenosis, ischemia, dyslipidemia, homozygous familial hypercholesterolemia, etc.), eye diseases such as retinitis pigmentosa, Leber congenital amaurosis, Leber hereditary optic neuropathy, and Stargardt disease; hereditary angioedema (HAE); lysosomal storage diseases such as San Filippo syndrome; hyperbilirubinemia such as CN type I or II or Gilbert's syndrome; Fabry disease, glycogen storage disease such as GSDI, GSDII (Pompe disease), GSDIII, GSDIV, GSDV, GSDVI, GSDVII, GSDVIII and lethal congenital glycogen storage disease of the heart. In some embodiments, the method further includes identifying a patient having any of the foregoing diseases or conditions. Such identification may be accomplished by, for example, sequencing the subject’s DNA, or based on phenotype (symptoms) associated with the disease or condition. [0109] In some embodiments, the method further comprises administering a nuclease. In some embodiments, the nuclease is selected from a CRISPR nuclease, a TALEN, a DNA-guided nuclease, a meganuclease, and a Zinc Finger Nuclease. In some embodiments, the CRISPR nuclease is Cas9, CasCpf1 (i.e., Cas12a), Cas12b (C2c1), Cas12f, C2c2 (i.e., Cas13a), C2c3, or C2c1 (i.e., Cas13b). In some embodiments, the DNA-guided nuclease is a NgAgo nuclease. In some embodiments, the nuclease is Cas9. [0110] In some embodiments, the method further includes a step of modulating transgene expression. In some embodiments, the synthetic AAV genome comprises at least two att sites as described herein. In some embodiments, modulating transgene expression includes administering a phage integrase or a nucleic acid encoding a phage integrase. In some embodiments, the nucleic acid is DNA or RNA, including mRNA. In some embodiments, the phage integrase is a ^, Bxb1, ICEclc, L5, P2, P22, HP1, ijC31, ijRv1, ijBT1, ijFC1, R4, TG1, ^MR11, A118, or TP901-1 phage integrase. In some embodiments, the phage integrase is Bxb1. In some embodiments, the phage integrase or nucleic acid encoding the phage integrase is incorporated into a delivery system. In some embodiments, the delivery system is a liposome. In some embodiments, the delivery system is a nanoparticle system. In some embodiments, the delivery system is a peptide. In some embodiments, the delivery system is a peptide. In some embodiments, the delivery system is an antibody. In some embodiments, the delivery system is an antibody subunit. In some embodiments, the delivery system is a lipid nanoparticle. Compositions [0111] In some embodiments, the AAV synthetic genome may be formulated as a composition for upregulating the expression of one or more additional genes. In some aspects, a synthetic AAV genome composition includes a synthetic AAV genome comprising an ITR sequence. In some embodiments, the synthetic AAV genome is produced by the method described herein. In some aspects, a composition includes a synthetic AAV genome as described herein. In some embodiments, the synthetic AAV genome comprises an expression cassette. [0112] In some embodiments, described herein is a composition including a synthetic AAV genome. In some embodiments, the synthetic AAV genome includes a 5’ ITR sequence, a truncated 3’ ITR sequence, a 3’ ITR sequence, and a truncated 5’ ITR sequence. In some embodiments, the synthetic AAV genome comprises an ITR sequence comprising at least one restriction enzyme half-site. In some embodiments, the synthetic AAV genome comprises a 5’ modified ITR sequence and a 3’ modified ITR sequence which comprise at least one restriction enzyme half-site. In some embodiments, the synthetic AAV genome comprises at least two att sites flanking a gene of interest, as further described herein. [0113] In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 1. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 2. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 3. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 4. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 1 and an ITR sequence of SEQ ID NO: 2. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 3 and an ITR sequence of SEQ ID NO: 4. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 1 and an ITR sequence of SEQ ID NO: 3. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 2 and an ITR sequence of SEQ ID NO: 4. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence of SEQ ID NO: 1, an ITR sequence of SEQ ID NO: 2, an ITR sequence of SEQ ID NO: 3, and an ITR sequence of SEQ ID NO: 4. [0114] In some embodiments, the synthetic AAV genome composition comprises an ITR sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 1. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 2. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 3. In some embodiments, the synthetic AAV genome composition comprises an ITR sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 4. [0115] In some aspects, a plasmid composition comprising an ITR sequence is described herein. In some embodiments, the plasmid composition comprises an ITR sequence of SEQ ID NO: 1. In some embodiments, the plasmid composition comprises an ITR sequence of SEQ ID NO: 2. In some embodiments, the plasmid composition comprises an ITR sequence of SEQ ID NO: 3. In some embodiments, the plasmid composition comprises an ITR sequence of SEQ ID NO: 4. In some embodiments, the plasmid composition comprises an ITR sequence of SEQ ID NO: 1 and an ITR sequence of SEQ ID NO: 2. In some embodiments, the plasmid composition comprises an ITR sequence of SEQ ID NO: 3 and an ITR sequence of SEQ ID NO: 4. [0116] In some aspects, a nucleic acid segment that encodes a synthetic AAV genome is provided herein. In some embodiments, the nucleic acid segment comprises a nucleotide sequence substantially as set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 4. In some embodiments, the nucleic acid segment comprises a modified ITR sequence comprising at least one restriction enzyme half-site. In some embodiments, the nucleic acid segment comprises at least two att sites flanking a gene of interest. [0117] In some aspects, a DNA segment with a single-stranded DNA overhang portion composition comprising an ITR sequence is described herein. In some embodiments, the DNA segment with a single-stranded DNA overhang portion composition comprises an ITR sequence of SEQ ID NO: 1. In some embodiments, the DNA segment with a single- stranded DNA overhang portion composition comprises an ITR sequence of SEQ ID NO: 2. In some embodiments, the DNA segment with a single-stranded DNA overhang portion composition comprises an ITR sequence of SEQ ID NO: 3. In some embodiments, the DNA segment with a single-stranded DNA overhang portion composition comprises an ITR sequence of SEQ ID NO: 4. In some embodiments, the DNA segment with a single-stranded DNA overhang portion composition comprises an ITR sequence of SEQ ID NO: 1 and an ITR sequence of SEQ ID NO: 2. In some embodiments, the DNA segment with a single-stranded DNA overhang portion composition comprises an ITR sequence of SEQ ID NO: 3 and an ITR sequence of SEQ ID NO: 4. [0118] In aspects, pharmaceutical compositions are provided. In some embodiments, the pharmaceutical composition comprises a synthetic AAV genome. In some embodiments, the synthetic AAV genome is produced using the synthetic process described herein and a pharmaceutically acceptable carrier or diluent. A synthetic AAV genome can be incorporated into pharmaceutical compositions suitable for administration to a subject for in vivo delivery to cells, tissues, or organs of the subject. Typically, the pharmaceutical composition comprises a synthetic AAV genome as disclosed herein and a pharmaceutically acceptable carrier. For example, synthetic AAV genome can be incorporated into a pharmaceutical composition suitable for a desired route of therapeutic administration (for example, parenteral administration). Passive tissue transduction via high pressure intravenous or intra-arterial infusion, as well as intracellular injection, such as intranuclear microinjection or intracytoplasmic injection, are also contemplated. Pharmaceutical compositions for therapeutic purposes can be formulated as a solution, microemulsion, dispersion, liposomes, or other ordered structure suitable to synthetic AAV genome concentration. Sterile injectable solutions can be prepared by incorporating the synthetically produced AAV genome in the required amount in an appropriate buffer with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization including a synthetic AAV genome can be formulated to deliver a transgene in the nucleic acid to the cells of a recipient, resulting in the therapeutic expression of the transgene or donor sequence therein. The composition can also include a pharmaceutically acceptable carrier. [0119] Pharmaceutically active compositions comprising synthetic AAV genome can be formulated to deliver a transgene for various purposes to the cell, for example, cells of a subject. [0120] Pharmaceutical compositions for therapeutic purposes typically must be sterile and stable under the conditions of manufacture and storage. The composition can be formulated as a solution, microemulsion, dispersion, liposomes, or other ordered structure suitable to high synthetically produced closed-ended DNA vector, for example, synthetic AAV genome concentration. Sterile injectable solutions can be prepared by incorporating the synthetically produced closed-ended DNA vector, for example, synthetic AAV genome in the required amount in an appropriate buffer with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. [0121] A synthetic AAV genome can be incorporated into a pharmaceutical composition suitable for topical, systemic, intra-amniotic, intrathecal, intracranial, intra- arterial, intravenous, intralymphatic, intraperitoneal, subcutaneous, tracheal, intra-tissue (for example, intramuscular, intracardiac, intrahepatic, intrarenal, intracerebral), intrathecal, intravesical, conjunctival (for example, extra-orbital, intraorbital, retroorbital, intraretinal, subretinal, choroidal, sub-choroidal, intrastromal, intracameral and intravitreal), intracochlear, and mucosal (for example, oral, rectal, nasal) administration. Passive tissue transduction via high pressure intravenous or intraarterial infusion, as well as intracellular injection, such as intranuclear microinjection or intracytoplasmic injection, are also contemplated. In some aspects, the methods provided herein comprise delivering one or more closed-ended DNA vector, including a synthetic AAV genome to a host cell. Also provided herein are cells produced by such methods, and organisms (such as animals, plants, or fungi) comprising or produced from such cells. Methods of delivery of nucleic acids can include lipofection, nucleofection, microinjection, biolistics, liposomes, immunoliposomes, polycation or lipidmucleic acid conjugates, naked DNA, and agent-enhanced uptake of DNA. [0122] Various techniques and methods are known in the art for delivering nucleic acids to cells. For example, synthetic AAV genome can be formulated into lipid nanoparticles (LNPs), lipidoids, liposomes, lipoplexes, or core-shell nanoparticles. Typically, LNPs are composed of nucleic acid (for example, synthetic AAV genome) molecules, one or more ionizable or cationic lipids (or salts thereof), one or more non-ionic or neutral lipids (for example, a phospholipid), a molecule that prevents aggregation (for example, PEG or a PEG- lipid conjugate), and optionally a sterol (for example, cholesterol). [0123] A synthetic AAV genome, such as one produced using the synthetic process as described herein, may be delivered to a cell by conjugating the nucleic acid with a ligand that is internalized by the cell. For example, the ligand can bind a receptor on the cell surface and internalized via endocytosis. The ligand can be covalently linked to a nucleotide in the nucleic acid. For example, a ligand may be a carbohydrate (including monosaccharide or polysaccharide), fatty acid, peptide, cholesterol, steroid, antibody, or antibody fragment. Exemplary conjugates for delivering nucleic acids into a cell are described, example, in WO2015/006740, WO2014/025805, WO2012/037254, WO2009/082606, WO2009/073809, WO2009/018332, WO2006/112872, WO2004/090108, WO2004/091515 and WO2017/177326. [0124] A synthetic AAV genome, such as one produced using the synthetic process as described herein, can also be delivered to a cell by transfection. Useful transfection methods include, but are not limited to, lipid-mediated transfection, cationic polymer- mediated transfection, or calcium phosphate precipitation. Transfection reagents are well known in the art and include, but are not limited to, TurboFect Transfection Reagent (Thermo Fisher Scientific), Pro-Ject Reagent (Thermo Fisher Scientific), TRANSPASS™ P Protein Transfection Reagent (New England Biolabs), CHARIOT™ Protein Delivery Reagent (Active Motif), PROTEOJUICE™ Protein Transfection Reagent (EMD Millipore), 293fectin, LIPOFECTAMINE™ 2000, LIPOFECT AMINE™ 3000 (Thermo Fisher Scientific), LIPOFECTAMINE™ (Thermo Fisher Scientific), LIPOFECTIN™ (Thermo Fisher Scientific), DMRIE-C, CELLFECTIN™ (Thermo Fisher Scientific), OLIGOFECTAMINE™ (Thermo Fisher Scientific), LIPOFECTACE™, FUGENE™ (Roche, Basel, Switzerland), FUGENE™ HD (Roche), TRANSFECTAM™(Transfectam, Promega, Madison, Wis.), TFX- 10™ (Promega), TFX-20™ (Promega), TFX-50™ (Promega), TRANSFECTIN™ (BioRad, Hercules, Calif.), SILENTFECT™ (Bio-Rad), Effectene™ (Qiagen, Valencia, Calif.), DC- chol (Avanti Polar Lipids), GENEPORTER™ (Gene Therapy Systems, San Diego, Calif), DHARMAFECT 1™ (Dharmacon, Lafayette, Colo ), DHARMAFECT 2™ (Dharmacon), DHARMAFECT 3™ (Dharmacon), DHARMAFECT 4™ (Dharmacon), ESCORT™ III (Sigma, St. Louis, Mo.), and ESCORT™ IV (Sigma Chemical Co.). Nucleic acids, such as neDNA, can also be delivered to a cell via microfluidics methods known to those of skill in the art. [0125] Methods of non-viral delivery of nucleic acids in vivo or ex vivo include electroporation, lipofection (see, U.S. Pat. No. 5,049,386; 4,946,787 and commercially available reagents such as Transfectam™ and Lipofectin™), microinjection, biolistics, virosomes, liposomes (see, for example, Crystal, Science 270:404-410 (1995); Blaese et al, Cancer Gene Ther.2:291-297 (1995); Behr et al, Bioconjugate Chem.5:382-389 (1994); Remy et al, Bioconjugate Chem. 5:647-654 (1994); Gao et al, Gene Therapy 2:710-722 (1995); Ahmad et al, Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787), immunoliposomes, polycation or lipidmucleic acid conjugates, naked DNA, and agent- enhanced uptake of DNA. Sonoporation using, for example, the Sonitron 2000 system (Rich- Mar) can also be used for delivery of nucleic acids. [0126] A synthetic AAV genome can also be administered directly to an organism for transduction of cells in vivo. Administration is by any of the routes normally used for introducing a molecule into ultimate contact with blood or tissue cells including, but not limited to, injection, infusion, topical application and electroporation. Suitable methods of administering such nucleic acids are available and well known to those of skill in the art, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective reaction than another route. [0127] Methods for introduction of a closed-ended DNA vector, including a synthetic AAV vector, can be delivered into hematopoietic stem cells, for example, by the methods as described, for example, in U.S. Pat. No.5,928,638. EXAMPLES [0128] The following examples are intended to illustrate details of the disclosure, without thereby limiting it in any manner. Example 1 – Producing Synthetic AAV Genomes [0129] The following example illustrates a method for producing a synthetic AAV genome. A CMV-GFP expression cassette is cloned into two separate AAV plasmids. The first AAV plasmid contained a modified AAV2 left ITR with 6 base pair EcoRV and AfeI half- sites and the first 54 bases of the right AAV2 ITR, as depicted in the embodiment of FIG.1A. The second AAV plasmid contained a modified AAV2 right ITR with 6 base pair EcoRV and AfeI half-sites and the first 54 bases the left ITR, as depicted in the embodiment of FIG. 1A. The plasmids were mixed in a 1:1 ratio and were cut with restriction enzymes EcoRV and AfeI to generate two DNA segments with complementary single-stranded DNA overhang portions, as shown in FIG. 1B. After the restriction enzyme digestion, the solution was heated to 95ÛC for 1 minute and allowed to cool slowly to room temperature, which allowed the complementary single-stranded overhang DNA portion from each segment to hybridize and form double-stranded synthetic AAV genomes with 2 nicks, as shown in FIG. 1C. T4 ligase was added to the solution at 25ÛC for 1.5 hours to ligate the two nicks in each synthetic AAV genome, as shown in FIG. 1D. T5 exonuclease was added at 37ÛC for one hour to purify the solution and degrade any plasmid backbone and mispaired DNA fragments. The solution was then applied to a DNA purification column to concentrate the synthetic AAV genome. The synthetic AAV genome was eluted from the DNA purification column. Example 2 – Producing Synthetic AAV Genomes [0130] The following example illustrates a method for producing a synthetic AAV genome. A CMV-GFP expression cassette was cloned into a first and a second AAV plasmid. Equal parts of AAV plasmid 1 and AAV plasmid 2 were mixed. The AAV plasmids were digested with EcoRV and AfeI at 37ÛC for 1 hour. Then, exonuclease V was added at 37ÛC for 30 minutes in order to degrade any contaminating linear and circular ssDNA and linear dsDNA, thereby removing the cut plasmid backbone and any of the original insert that re- hybridized, without degrading closed-ended linear nicked dsDNA. T4 ligase was added at 37ÛC for 30 minutes to seal nicks left by the EcoRV and AfeI restriction enzymes. T5 exonuclease was added at 37ÛC for 30 mins in order to degrade linear and circular ssDNA and linear and nicked circular dsDNA (any remaining nicked DNA non-ligated products). [0131] The synthetic AAV genome was then purified by application and elution from a DNA purification column (NucleoSpin Gel and PCR Clean^up, available from Macherey-Nagel). FIG. 2 depicts a gel electrophoresis showing the final product synthetic AAV genome. In FIG.1, lane 1 shows a molecular weight standard. Lane 2 is the synthetic AAV genome resistant to exonuclease. Lane 3 is the exonuclease-resistant synthetic AAV genome after digestion with HindIII. Lane 4 is an exonuclease-sensitive synthetic AAV genome after digestion with HindIII, . Example 2 – Cell Study [0132] The following example illustrates a cellular study of the synthetic AAV genomes containing a CMV-GFP expression cassette produced using the methods described in Example 1. HeLa cells were transfected with either 300 ng of synthetic AAV genomes containing the CMV-GFP expression cassette or 300 ng of plasmid DNA containing the CMV- GFP expression cassette. [0133] A set of microscope images were taken of the GFP expression found in HeLa cells transfected with synthetic AAV genomes containing the CMV-GFP expression cassette and HeLa cells transfected with plasmid DNA containing the CMV-GFP expression cassette, as shown in FIG. 3. The HeLa cells transfected with the synthetic AAV genomes maintained high GFP expression over the 8 days of the experiment, while HeLa cells transfected with the plasmid displayed decreasing amounts of GFP expression starting at day 5. This experiment demonstrated that cells transfected with synthetic AAV genomes had transgene expression lasting over longer period of time in comparison to cells transfected with plasmids. Example 3 – Synthetic AAV-ABCA4 [0134] The following example illustrates a synthetic AAV genome that may be constructed using methods described herein. [0135] A synthetic AAV genome carrying the 6,822 bp human ABCA4 gene was constructed using methods described herein. FIG. 5A depicts the synthetic AAV-ABCA4 molecule including various components of the payload and left and right ITRs. The ABCA4 gene payload of the synthetic AAV genome shown in Fig. 5A was about 2 times larger than the carrying capacity of a standard AAV vector, which is approximately 4.7 kb. FIG.5B is an image of a gel electrophoresis experiment showing the final product synthetic AAV-ABCA4 genome at approximately 8,872 bp. Example 4- Promoterless Synthetic AAV [0136] The following example illustrates a cellular study of an AAV vector comprising a GFP expression cassette produced using the methods described herein. An expression cassette, including a gene expressing GFP was interested into a synthetic AAV genome by the methods described above. [0137] HepG2 cells were transfected with the synthetic AAV genomes containing the GFP gene flanked by wildtype genomic DNA corresponding to a locus downstream of the ALB gene. The synthetic AAV genomes did not include a promoter. As shown in FIG.6, GFP expression of the HepG2 cells was observed over seven days, during which time GFP expression steadily increased. This experiment demonstrated that transfection with a promoterless synthetic AAV genome can result in stably integrated GFP under control of the ALB gene locus. Example 5 – Treatment using Synthetic AAV-ABCA4 for Stargardt’s Disease [0138] The following example illustrates a method of treatment using synthetic AAV genomes such as those prepared by the methods described herein. [0139] The synthetic AAV-ABCA4 genome described in Example 3 is formulated with a lipid nanoparticle and is administered to a subject suffering from Stargardt’s disease via intraocular injection. Administration of the synthetic AAV-ABCA4 genome treats the Stargardt’s disease. Example 6- Treatment by Correcting Point Mutation via Synthetic AAV Genome [0140] The following example illustrates a method of treatment using synthetic AAV genomes such as those prepared by the methods described herein. [0141] A synthetic AAV genome is constructed which includes 2,000 bp of wild- type genomic DNA centered on a point mutation to correct. A disease or condition involving a point mutation, such as cystic fibrosis or sickle cell, is treated by transfecting a human cell with the synthetic AAV genome. As depicted in FIG. 8A, homologous recombination occurs with the cell’s DNA and the synthetic AAV genome, and the point mutation is corrected, thereby treating the disease. Example 7- Treatment by Correcting Indel via Synthetic AAV Genome [0142] The following example illustrates a method of treatment using synthetic AAV genomes such as those prepared by the methods described herein. [0143] A synthetic AAV genome is constructed which includes 2,000 bp of wild- type genomic DNA centered on an indel to correct. A disease or condition involving an indel, such as Stargardt’s type 3 disease, is treated by transfecting a human cell with the synthetic AAV genome. As depicted in FIG.8B, homologous recombination occurs with the cell’s DNA and the synthetic AAV genome, and the indel is corrected, thereby treating the disease. Example 8- Treatment by Gene Addition via Synthetic AAV Genome [0144] The following example illustrates a method of treatment using synthetic AAV genomes such as those prepared by the methods described herein. [0145] A synthetic AAV genome is constructed which includes 1,000 bp of wild- type genomic DNA flanking a therapeutic gene. A disease or condition involving an gene deficiency, such as ELOVL2 deficiency, is treated by transfecting a human cell with the synthetic AAV genome. As depicted in FIG. 8C, homologous recombination occurs with the cell’s DNA and the synthetic AAV genome, and the gene of interest is added, thereby treating the disease. Example 9- Treatment by Correcting Point Mutation via Synthetic AAV Genome and Nuclease [0146] The following example illustrates a method of treatment using synthetic AAV genomes such as those prepared by the methods described herein. [0147] A synthetic AAV genome is constructed which includes 2,000 bp of wild- type genomic DNA centered on a point mutation to correct. A disease or condition involving a point mutation, such as cystic fibrosis or sickle cell, is treated by transfecting a human cell with the synthetic AAV genome, with the addition of a nuclease such as Cas9. As depicted in FIG. 8D, homologous recombination occurs with the cell’s DNA and the synthetic AAV genome, and the point mutation is corrected, thereby treating the disease. The addition of the nuclease results in an increase in efficiency several fold. Example 10- Modulating Synthetic AAV Expression [0148] The following example illustrates a cellular study of synthetic AAV genomes that may modulated after administration to reduce expression. [0149] A synthetic AAV genome was constructed using methods described herein with att sites flanking the expression cassette containing a gene of interest (GOI). HeLa cells were transfected with the synthetic AAV genome and expression was allowed for 48 hours. Then the HeLa cells were transfected with varying amounts of a lipid nanoparticle (LNP) containing phage integrase Bxb1 mRNA. Transgene expression was determined by qPCR. As shown in FIG. 7A, up to an approximately 70% reduction in expression was achieved. This experiment demonstrated that transgene expression levels can be modulated, as illustrated in the schematic depicted in FIG. 7B. Other Considerations [0150] It should be appreciated that all combinations of the foregoing concepts and additional concepts discussed in greater detail below (provided such concepts are not mutually inconsistent) are contemplated as being part of the inventive subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are contemplated as being part of the inventive subject matter disclosed herein. It should also be appreciated that terminology explicitly employed herein that also may appear in any disclosure incorporated by reference should be accorded a meaning most consistent with the particular concepts disclosed herein. [0151] Reference throughout the specification to “one example”, “another example”, “an example”, and so forth, means that a particular element (such as, feature, structure, and/or characteristic) described in connection with the example is included in at least one example described herein, and may or may not be present in other examples. In addition, it is to be understood that the described elements for any example may be combined in any suitable manner in the various examples unless the context clearly dictates otherwise. [0152] It is to be understood that the ranges provided herein include the stated range and any value or sub-range within the stated range, as if such value or sub-range were explicitly recited. For example, a range from about 90°C to about 100°C should be interpreted to include not only the explicitly recited limits of from about 90°C to about 100°C, but also to include individual values, such as about 91.5°C, about 99°C, about 93.2°C, etc., and sub-ranges, such as from about 93°C to about 97°C, etc. Furthermore, when “about” and/or “substantially” are/is utilized to describe a value, this is meant to encompass minor variations (up to +/- 10%) from the stated value. [0153] While several examples have been described in detail, it is to be understood that the disclosed examples may be modified. Therefore, the foregoing description is to be considered non-limiting. [0154] While certain examples have been described, these examples have been presented by way of example only, and are not intended to limit the scope of the disclosure. Indeed, the novel methods described herein may be embodied in a variety of other forms. Furthermore, various omissions, substitutions and changes in the methods described herein may be made without departing from the spirit of the disclosure. The accompanying claims and their equivalents are intended to cover such forms or modifications as would fall within the scope and spirit of the disclosure. [0155] Features, materials, characteristics, or groups described in conjunction with a particular aspect, or example are to be understood to be applicable to any other aspect or example described in this section or elsewhere in this specification unless incompatible therewith. All of the features disclosed in this specification (including any accompanying claims, abstract and drawings), and/or all of the steps of any method or process so disclosed, may be combined in any combination, except combinations where at least some of such features and/or steps are mutually exclusive. The protection is not restricted to the details of any foregoing examples. The protection extends to any novel one, or any novel combination, of the features disclosed in this specification (including any accompanying claims, abstract and drawings), or to any novel one, or any novel combination, of the steps of any method or process so disclosed. [0156] Furthermore, certain features that are described in this disclosure in the context of separate implementations can also be implemented in combination in a single implementation. Conversely, various features that are described in the context of a single implementation can also be implemented in multiple implementations separately or in any suitable sub-combination. Moreover, although features may be described above as acting in certain combinations, one or more features from a claimed combination can, in some cases, be excised from the combination, and the combination may be claimed as a sub-combination or variation of a sub-combination. [0157] Moreover, while operations may be depicted in the drawings or described in the specification in a particular order, such operations need not be performed in the particular order shown or in sequential order, or that all operations be performed, to achieve desirable results. Other operations that are not depicted or described can be incorporated in the example methods and processes. For example, one or more additional operations can be performed before, after, simultaneously, or between any of the described operations. Further, the operations may be rearranged or reordered in other implementations. Those skilled in the art will appreciate that in some examples, the actual steps taken in the processes illustrated and/or disclosed may differ from those shown in the figures. Depending on the example, certain of the steps described above may be removed or others may be added. Furthermore, the features and attributes of the specific examples disclosed above may be combined in different ways to form additional examples, all of which fall within the scope of the present disclosure. [0158] For purposes of this disclosure, certain aspects, advantages, and novel features are described herein. Not necessarily all such advantages may be achieved in accordance with any particular example. Thus, for example, those skilled in the art will recognize that the disclosure may be embodied or carried out in a manner that achieves one advantage or a group of advantages as taught herein without necessarily achieving other advantages as may be taught or suggested herein. [0159] Conditional language, such as “can,” “could,” “might,” or “may,” unless specifically stated otherwise, or otherwise understood within the context as used, is generally intended to convey that certain examples include, while other examples do not include, certain features, elements, and/or steps. Thus, such conditional language is not generally intended to imply that features, elements, and/or steps are in any way required for one or more examples or that one or more examples necessarily include logic for deciding, with or without user input or prompting, whether these features, elements, and/or steps are included or are to be performed in any particular example. [0160] Conjunctive language such as the phrase “at least one of X, Y, and Z,” unless specifically stated otherwise, is otherwise understood with the context as used in general to convey that an item, term, etc. may be either X, Y, or Z. Thus, such conjunctive language is not generally intended to imply that certain examples require the presence of at least one of X, at least one of Y, and at least one of Z. [0161] Language of degree used herein, such as the terms “approximately,” “about,” “generally,” and “substantially” represent a value, amount, or characteristic close to the stated value, amount, or characteristic that still performs a desired function or achieves a desired result. [0162] The scope of the present disclosure is not intended to be limited by the specific disclosures of examples in this section or elsewhere in this specification, and may be defined by claims as presented in this section or elsewhere in this specification or as presented in the future. The language of the claims is to be interpreted broadly based on the language employed in the claims and not limited to the examples described in the present specification or during the prosecution of the application, which examples are to be construed as non- exclusive.