# Patent

## Title
High throughput system for producing recombinant viruses using site-specific recombination

## Abstract

Disclosed are the methods for producing recombinant viruses using site-specific recombination in vitro. In the present invention, circular viral genomic DNAs are digested with restriction enzymes to generate a linear form viral genomic DNAs flanked by site-specific recombination sites, and then are subjected to site-specific recombination with the desired genomic materials flanked by site-specific recombination sites in vitro. According to the present invention, since the site-specific recombination mixture can be applied to host cells without further procedures of selecting the desired recombinant viral genomic DNAs, it is possible to obtain numerous recombinant viruses rapidly at the same time. Thus, the present invention can be used as a high throughput system for generating and screening hundreds or thousands of recombinant viruses.

## Background
CROSS-REFERENCE TO OTHER APPLICATIONS
Priority is claimed from Korean Patent Application No. 2002-12634, filed on Mar. 9, 2002.
BACKGROUND OF THE INVENTION
1. Field of the Invention
This invention relates to a method for producing recombinant viruses and vectors for the same. Furthermore, this invention relates to deoxyribonucleic acid (DNA) constructs for the method and the recombinant viruses produced by the method.
2. Description of the Related Art
A recombinant viral vector means a genetically engineered vector, which is used in, for example: the preparation of a vaccine; analysis of function of a gene, a group of genes, or a genomic domain; production of proteins; and gene therapy. Genomic materials, which can be integrated into a viral vector, include any genomic materials such as a gene, cDNA, genomic DNA, DNA sequences encoding peptides or proteins, ribonucleic acid (RNA), anti-sense RNA, siRNA, DNA for si RNA, a promoter, or an enhancer. A virus, which is used in the preparation of a vector, includes baculovirus, adenovirus, adeno-associated virus (AAV), retrovirus, Herpes virus, hepatitis B virus (HBV), polioma virus, sindbid virus, and vaccinia virus.
Retroviruses are known as one of the most widely used viruses in gene therapy. See Patience, C., et al., Packaging of Endogenous Retroviral Sequences in Retroviral Vectors Produced by Murine and Human Packaging Cells, J. Virol, April 1998, pp. 2671-2676, Vol. 72, No. 4; Marshall, E., Gene Therapy's Growing Pains, Science, Aug. 25, 1995, pp. 1050-1055, Vol. 269. Retroviral genomes have two long terminal repeats (LTRs), capsid sequences and 3 (three) coding regions (gag, pol and env), and the method of preparation and their use in vitro and in vivo have been disclosed. See WO9908692A1 and EP 453242. The clinical application of a retroviral vector, however, has the following disadvantages: it forms a replication-competent retrovirus (RCR) (see Powell, S. K., et al., Efficacy of Antiretroviral Agents Against Murine Replication-Competent Retrovirus Infection in Human Cells, J. Virol., October 1999, pp. 8813-8816, Vol. 73, No. 10); it has a relatively lower level of gene expression, and the level decreases continuously in vivo; and the titer of virus is low. Furthermore, the retrovirus cannot transfer a gene to a non-dividing cell. See Jaffee, E. M., et al., High Efficiency Gene Transfer into Primary Human Tumor Explants Without Cell Selection, Cancer Research, 1993, pp. 2221-2226, Vol. 53, Issue 10; Bender, M. A., et al., Evidence that the Packaging Signal of Moloney Murine Leukemia Virus Extends into the gag Region, J. Virol., May 1987, pp. 1639-1646, Vol. 61, No. 5.
An adenovirus has a linear genome (sized about 36 kb) and includes replication origin and capsid signals near to the left inverse terminal region (ITR) (103 bp). See Shenk, T., Adenoviridae: The Viruses and Their Replication, Fields Virology, 3rd Ed., 1996, pp. 2111-2148. Usually, adenoviral vectors have been made by deleting the E1 site of the viral genome, which is essential for viral replication. The vector includes foreign genomic material substituting the E1 site, which are transferred to packaging cells which provide E1 proteins. As a result, viral replication occurs only in the packaging cells. Representative packaging cells include, for example, HEK 293 cell, 911 cell, and PER.C6 cells. See Hitt, M. M., et al., Human Adenovirus Vectors for Gene Transfer into Mammalian Cells, Advances in Pharmacology, 1997, pp. 137-206, Vol. 40; Wang, Y., et al., Adenovirus Technology for Gene Manipulation and Functional Studies, Drug Discovery Today, January 2000, pp. 10-16, Vol. 5, No. 1. An adenoviral vector has advantages such as safety, affinity to various cells, possibility of infecting dividing cells and higher titer (1011 pfu/ml). Thus, adenoviruses have been used in the preparation of a vector expressing heterologous genes.
Adeno-associated virus (sized about 4700 bp) has ITRs (sized about 145 bp) as replication origins at each terminus. It can be integrated into the genomic DNA of various types of host cells safely and specifically.
In order to use a recombinant virus as a vector, it should be modified not to replicate in the infected cells. Therefore, so-called “defective viruses”, which have deletions of some essential regions of genome for viral replication, are usually employed in the preparation of recombinant viral vectors. In a retrovirus, for example, gag, pol and/or env genes are deleted, and the regions are replaced with desired genomic materials. See Bender, M. A., et al., Evidence that the Packaging Signal of Moloney Murine Leukemia Virus Extends into the gag Region, J. Virol., May 1987, pp. 1639-1646, Vol. 61, No. 5. For an adenovirus, the E1, E2 and/or E4 sites are deleted for the preparation of a viral vector. See Levrero, M., et al., Defective and Nondefective Adenovirus Vectors for Expressing Foreign Genes It Vitro and In Vivo, Gene, 1991, pp. 195-202, Vol. 101; Ghosh-Choudhury, G., et al., Human Adenovirus Cloning Vectors Based on Infectious Bacterial Plasmids, Gene, 1986, pp. 161-171, Vol. 50. Additionally, a pseudo-virus vector, which consists of only the essential regions (such as, ITR and capsid sequences) of the replication, has also been used for obtaining recombinant viruses. See WO95/02697.
In addition, baculoviruses, which are known as having circular genomic DNA, have been used for the preparation of viral vectors. Baculoviridae are infectious in invertebrates, such as insects and crustacea. Autographa californica nuclear polyhedrosis virus (AcNPV) is one of the most widely used baculoviruses, and it contains double-stranded circular genomic DNA (sized about 134 kb) (GenBank: NC—001623). Smith et al. developed recombinant baculoviruses by inserting β-interferon genes, and successfully obtained interferon proteins from insect cells using the recombinant baculoviruses. See Smith, G. E., et al., Production of Human Beta Interferon in Insect Cells Infected with a Baculovirus Expression Vector, Molecular and Cellular Biology, December 1983, pp. 2156-2165, Vol. 3, No. 12. Since then, numerous genes have been expressed and produced using a recombinant baculoviral system. The features of the methods are that: i) it is possible to produce desired recombinant baculoviruses at high efficiency by employing polyhedrin promoter; and ii) it can be used for the expression of genes that do not exhibit their activities when incubated in bacteria. This is due to that post-translational modification is carried out in insect cells. However, the size of the genome of baculovirus made it difficult to engineer the genome through the conventional restriction and ligation method. Therefore, homologous recombination has been used in insect cells generally. In order to conduct homologous recombination, carrier vectors containing desired genes and nucleic acid sequences necessary for the homologous recombination are prepared. Then, insect cells are transfected with the carrier vectors and viral genomic DNA to induce recombination. In that method, however, since the production efficiency of recombinant viruses is relatively low (0.1-2%), repetitive screening of baculoviral plaques should be performed in order to obtain the desired recombinant viruses. Thus, it is also considered as being an inefficient method.
Kitts et al. disclosed an improved method that increased production efficiency of recombinant viruses. See Kitts, P. A., Linearization of Baculovirus DNA Enhances the Recovery of Recombinant Virus Expression Vectors, Nucleic Acids Research, 1990, pp. 5667-5672, Vol. 18, No. 19. They made baculoviral genomic DNA to be in linear form using a restriction enzyme. In the Kitts' method, a linker, which includes Bsu36I recognition base sequences, CCTNAGG, or lacZ genes, is inserted into wild-type AcNPV genome at the polyherin locus in order to introduce Bsu36I site recognition nucleic acid sequences. Next, the viral DNA is digested with Bsu36I restriction enzyme, and then transferred to insect cells together with carrier vectors containing desired genomic materials so as to induce homologous recombination. The production efficiency of the desired recombinant viruses is from 26% to 44%. According to that method, linear digested DNA segments, which are not subjected to recombination, are excluded selectively from the production of viral vectors. Thus, the desired recombinant viruses expressing desired protein can be generated with relatively high efficiency. However, the method has disadvantages as follows: i) it is not possible to digest Bsu36I recognition sites up to 100% and ii) since the digested DNA segments are fused with each other in insect cells by ligase, selection procedures for the desired viral vectors need to be employed.
Peakman et al. provided another method using site-specific recombination of cre/loxP system in vitro. See Peakman, T. C., et al., Highly Efficient Generation of recombinant Baculoviruses by Enzymatically Mediated Site-Specific In vitro Recombination, Nucleic Acids Research, pp. 495-500, Vol. 20, No. 3. Briefly, they prepared baculoviruses containing loxP sites and applied them to site-specific recombination in vitro with desired genomic materials by reacting the viruses with transfer vectors having the genomic materials flanked with loxP sites, in the presence of cre recombination enzyme. In that method, the time-period for producing recombinant viruses is shortened. However, the production efficiency of desired recombinant viruses is still low (0.2% to 49%), thereby it is not suitable to be used as a high-throughput system for the preparation of recombinant viruses.
In addition, Luckow et al. reported a method of inserting a desired genomic cassette into a baculoviral genome by site-specific recombination in a cell. See Luckow, V. A., et al., Efficient Generation of Infectious Recombinant Baculoviruses by Site-Specific Transposon-Mediated Insertion of Foreign Genes into a Baculovirus Genome Propagated in Escherichia coli, J. Virol., August 1993, pp. 4566-4579, Vol. 67, No. 8. According to Luckow's method, a shuttle vector (sized about 130 kb) is prepared by inserting a plasmid replication origin, which replicates in bacteria, including kanamycin resistance gene and attTn7 recombination sequences, into baculoviral genome. The shuttle is named “Bacmid.” DH10Bac was generated by transforming E. coli with Bacmid and a helper plasmid, which in turn was transformed using a plasmid containing desired genes and polyhedrin promoter to prepare recombinant Bacmid in E coli. The resulting recombinant Bacmid is isolated and transferred to insect cells to obtain recombinant viruses. According to that method, baculoviruses can be obtained with relatively high efficiency by using site-specific recombination of transposon. That method, however, required complex procedures, for example, cloning desired genomic materials to Tn7 Bacmid carrier vectors; transforming DH10Bac for the recombination of Tn7 baculoviruses; selecting and isolating bacteria having Bacmid that contains the desired genomic material; purifying Bacmid DNA (sized about 130 kb) from the isolated bacteria; and transferring the DNA again to insect cells to produce recombinant virues.
Thus, non of the above-mentioned methods of the prior art have provided suitable ways to overcome the problems of a relatively long time-period in preparing recombinant viruses (about 3 to 6 weeks) and low production efficiency. Therefore, there has been a demand for the development of an improved method.
In this regard, we have carried out studies to produce recombinant viruses having a desired genomic material more rapidly and efficiently. In one embodiment, we prepared recombinant viral vectors in vitro using site-specific recombination and employing the vectors to produce recombinant viruses. Since the viral vectors obtained in vitro according to this invention can be applied to animal cells directly without further procedures like selection, the present invention not only simplifies the total procedure significantly but also provides desired recombinant viruses with up to 100% production efficiency. Thus, higher virus titer can be obtained according to the present invention.
SUMMARY OF THE INVENTION
Any publications referenced herein are hereby incorporated by reference in this application in order to more fully describe the state of the art to which the present invention pertains.
To understand the present invention, it is important to note that all technical and scientific terms used herein, unless otherwise defined, are intended to have the same meaning as commonly understood by one of ordinary skill in the art. The techniques used herein are also those that are known to one of ordinary skill in the art, unless stated otherwise.
Reference to particular buffers, media, reagents, cells, culture conditions and the like, or to some subclass of same, is not intended to be limiting, but should be read to include all such related materials that one of ordinary skill in the art would recognize as being of interest or value in the particular context in which that discussion is presented. For example, it is often possible to substitute one buffer system or culture medium for another, such that a different but known way is used to achieve the same goals as those to which the use of suggested method, material or composition is directed.
It is an object of this invention to provide more rapid and efficient method for producing recombinant viruses.
In order to accomplish this object, this invention employs recombinant viral vectors that are prepared in vitro by site-specific recombination.
In the present invention, viral genomic DNA is made in linear form by restriction enzymes before being applied to site-specific recombination in vitro. Since linear viral genomic DNA, which is not subjected to the site-specific recombination, cannot replicate by itself, almost all of the expressed viruses are believed to be those from the circular viral genomic DNA. Thus, according to the present invention, it is possible to obtain recombinant viruses at high efficiencies without the procedures for selecting and isolating the desired recombinant viruses. Accordingly, the method of the present invention can be applied to a virus having circular genomic DNA, for example, polioma virus, papiloma virus and hepatitis B virus.
Site-specific recombination is an event occurring naturally in various living organisms. Enzymes for the site-specific recombination contain not only endonuclease activity, but also ligase activity, so they recognize a certain part of DNA sequences and replace it with any other corresponding DNA sequence. See Yang, W., et al., Site-Specific Recombination in Plane View, Structure, Nov. 15, 1997, pp. 1401-1406, Vol. 5. Int/att system from bacterio λ phage, Cre/LoxP system from P1 bacteriophage and FLP-FRT system from yeast are well developed site-specific recombination systems.
Site-specific recombination systems have been used in i) expression control of desired genomic materials cloned into recombinant viruses, ii) excising helper-virus when preparing helper-viral dependent viruses, iii) increasing the efficiency of homologous recombination in packaging cells, or iv) inducing site-specific recombination between carrier vectors and viral genome in packaging cells to prepare recombinant viruses. See Ng, P., et al., Yeast Recombinase FLP Functions Effectively in Human Cells for Construction of Adenovirus Vectors, BioTechniques, September 2000, pp. 524-528, Vol. 29, No. 3; Ng, P., et al., A High-Efficiency Cre/loxP-Based System for Construction of Adenoviral Vectors, Human Gene Therapy, Nov. 1, 1999, pp. 2667-2672, Vol. 10; Hardy, S., et al., Construction of Adenovirus Vectors Through Cre-lox Recombination, J. Virol., March 1997, pp. 1842-1849, Vol. 71, No. 3; Parks, R. J., et al., A Helper-Dependent Adenovirus Vector System: Removal of Help Virus by Cre-mediated Excision of the Viral Packaging Signal, Proc. Natl. Acad. Sci. USA, November 1996, pp. 13565-13570, Vol. 93. However, the said applications of the site-specific recombination disclosed in the prior art were merely indirect and supplementary uses in vivo or in a cell line, not in vitro.
In addition, applications of site-specific recombination in the preparation of recombinant viruses having circular genomic DNA were reported: i) in the preparation of recombinant baculoviruses in bacteria using Tn7 recombination, and ii) in the preparation of recombinant baculoviruses using a cre/lox-P system in vitro.
However, there have been no applications of site-specific recombination in vitro for specific insertion of desired genomic materials into viral genomic DNA in order to obtain recombinant viral vectors. In particular, there have been no applications to prevent the expression of viral genomic DNA that do not contain desired genomic materials. Thus, the present invention is characterized by employing site-specific recombination in preparing recombinant viral vectors in vitro. The present invention has unexpected advantages compared to the prior art as follows: i) it is possible to obtain recombinant viral vectors more easily and more rapidly by employing site-specific recombination in vitro; ii) it does not require any further procedure of selecting desired recombinant viruses from intermediate host cells, since the viral genomic DNA is made in linear form and thereby the linear viral DNA, which do not form in circular form by integration of the desired genomic materials, cannot be expressed; and iii) it is possible to generate the same kind of genomic materials from various types of viruses or to generate various genomic materials from the same kind of viral type multi-well (e.g., 96-well or 384-well) by employing a common transfer vector containing an expression cassette that does not have DNA from a viral genome.
Furthermore, according to the present invention, homologous recombination in the packaging cells is not required. Also a particular cell line for inducing homologous recombination is not required. Table I and Table 2 show the results of the comparisons between the method of the present invention (BacHTS system) and the methods of the prior art (BacPAK6 system and BacToBac system) with regard to the processes. With the results, it is clear that the desired recombinant viruses can be obtained even more rapidly by using the method of this invention in comparison to the prior art.







TABLE 1







The comparison of the number of procedures between the method


of the present invention and the methods of prior art.











the number of procedures
Days
time-period














BacPAK6 system
11
6
10


BacToBac system
13
8
12


BacHTS system
5
3
7
















TABLE 2







The comparison of the processes required for preparation


of baculoviruses.









BacPAK6 system
BacToBac system
BacHTS system















1.
RE cut
1.
LR reaction
1.
Recombination


2.
Agarose gel elution
2.
Transformation
2.
Transfection


3.
Ligation
3.
Colony seeding
3.
Infection


4.
Transformation
4.
Plasmid purifica-
4.
Harvest and virus





tion

storage


5.
Colony seeding
5.
RE analysis
5.
Protein expres-







sion analysis


6.
Plasmid purification
6.
DH10Bac





transformation


7.
RE analysis
7.
Streaking


8.
Transfection
8.
Seeding


9.
Infection
9.
Bacmid





purification


10.
Harvest and virus
10.
Transfection



storage


11.
Protein expression
11.
Infection



analysis




12.
Harvest and virus





storage




13.
Protein expres-





sion analysis









Furthermore, according to the present invention, since the promoter for the expression of the desired genomic materials, and the fusion system and the polyadenyl sequences for the preparation of a fusion protein are provided from the parent viral genome, the gene cassette cloned to a common carrier vector can be applied to produce various types of viruses.
Thus, the present invention provides significantly useful tools for studying functions of genes, of which demand has been increasing greatly since the completion of the genome project. See Wang, Y., et al., Adenovirus Technology for Gene Manipulation and Functional Studies, Drug Discovery Today, January 2000, pp. 10-16, Vol. 5, No. 1.
In one embodiment, the present invention employs baculovirus having circular genomic DNA, and an Int/att system from bacteriophage λ (Genebank: NC 001416) as a site-specific recombination system. In the Int/att system, attR site-specific recombination sites within a viral genomic DNA fragment react with corresponding attL site-specific recombination sites, including desired genomic materials from a carrier vector, in the presence of λ integrase recombination enzyme, integration host factor (1HF) as a co-factor and Xis, and result in a vector DNA fragment containing attB and attP sites. See Hartley, J. L., et al., DNA Cloning Using In Vitro Site-Specific Recombination, Genome Research, 2000, pp. 1788-1795, Vol. 10. Other recombination systems from various organisms, for example, the cre/loxP system from bacteriophage P1, and the FLP/FRT system from the Saccharomyces cerevisiae 21t circle plasmid, can be employed.
When the mixture is transferred directly to suitable host cells, which are expected to express desired recombinant viruses, only the circular viral genomic DNA containing attB1-[desired genomic materials]-attB2 can replicate and form viral particles. The linear viral DNA fragment and the vector DNA itself, which do not react with each other, and the circular viral DNA having attP sites cannot replicate and cannot form viral particles. In FIG. 1, site-specific recombination between a gene cassette and vBacHTS baculoviral DNA in vitro is presented.
In another embodiment, vBacHTS viral DNA is constructed to include site-specific recombination sequences and Bsu36I recognition base sequences, which in turn are made to linear form viral DNA flanked by 2 (two) site-specific sites with treatment of Bsu36I restriction enzyme. The linear vBacHTS DNA cannot form viral particles since the vBacHTS viral DNA is digested at 2 (two) Bsu36I recognition sites having nucleic acid sequences different from each other, while the circular form DNA generated by site-specific recombination formed viral particles efficiently.
In another embodiment, the reaction mixture containing viral DNA having desired genomic materials, which is integrated by site-specific recombination, is transferred to Sf21 insect cells, and then viral packaging is detected. Thus, according to the present invention, recombinant viruses can be obtained without employing intermediate host cells, such as E. coli or yeast, for selecting and amplifying suitable genomic DNA. Therefore, the recombinant viruses are suitable for the purpose of expressing desired genes from host cells. The activity measurement of GFP and GUS proteins indicates that the method of the present invention is more efficient than the method of the prior art.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 illustrates gene-screening processes using BacHTS system.
FIG. 2 depicts the cleavage map of pBacHTS.
FIG. 3 depicts the cleavage map of pBacHTS2.
FIG. 4 depicts the cleavage map of pBacPAK8_attR1.
FIG. 5 depicts the cleavage map of pBacPAK_attR1R2.
FIG. 6 depicts the cleavage map of pBacHTS_GFP.
FIG. 7 depicts the cleavage map of pBacHTS Flag.
FIG. 8 depicts the cleavage map of pBacHTS_His.
FIG. 9 depicts the cleavage map of pBacHTS_HisGst.
FIG. 10 depicts the cleavage map of pBacHTS_Gst.
FIG. 11 depicts the cleavage map of pBacHTS2_EGFP.
FIG. 12 depicts the cleavage map of pEntr_EGFP.
FIG. 13 illustrates the process of preparation of vBacHTS virus.
FIG. 14 illustrates the process of preparation of bBacHTS2 clone.
FIG. 15 shows the map of baculoviral polyhedrin locus.
FIG. 16 illustrates agarose gel electrophoretic analysis of vBacHTS viral DNA and bBacHTS2 viral DNA.
FIG. 17 illustrates procedures for the preparation of desired recombinant viruses using vBacHTS and a gene cassette.
FIG. 18 shows the results of activity assays of GFP baculoviruses and GUS recombinant viruses in a vBacHTS system.
FIG. 19 shows plaque assays for GFP baculoviruses and GUS recombinant viruses in a vBacHTS system.
FIG. 20 shows the results of activity assays of GFP baculoviruses in a bBacHTS2 system.
FIG. 21 shows the results of activity assays of GUS recombinant baculoviruses in a bBacHTS2 system.
FIG. 22 illustrates a GFP image in multi-well plate and the results of western blot.
FIG. 23 shows enzyme activity using X-Gluc of GUS recombinant viruses in a multi-well plate.
FIG. 24 shows the results of site-specific recombination in vitro.
FIG. 25 depicts expression of GFP-LacZ fusion proten in Sf21 cells after 4 days from the transfer of recombinant DNA to the cells.
FIG. 26 shows the results of western blot of the expression of GFP-LacZ fusion protein using SDS-PAGE and GFP antibodies.
FIG. 27 depicts LacZ enzyme activity in recombinant virus (GFP-LacZ) using X-Gal substrates.
FIG. 28 shows the image of Sf21 cells infected with GFP—YPK baculoviruses from a multi-well plate.
FIG. 29 shows the results of screening protein kinase (Rb, Histone H1, MBP).
FIG. 30 depicts phosphorylation of Rb (retinoblastoma) protein.
FIG. 31 illustrates phosphorylation of Rb protein by #2-A9 protein kinase.



DESCRIPTION OF THE PREFERRED EMBODIMENTS
Preferred embodiments of this invention are described in the following examples. Other embodiments within the scope of the claims herein will be apparent to those skilled in the art from consideration of the specification or practice of the invention as disclosed herein. It is intended that the specification, together with the examples, be considered exemplary only, with the scope and the spirit of the invention being indicated by the claims which follow the examples. The examples herein are meant to exemplify the various aspects of carrying out the invention and not intended to limit the scope of the invention in any way. The examples do not include detailed descriptions of conventional methods employed, such as in the performance of genomic DNA isolation, polymerase chain reaction (PCR), and sequencing procedures. Such methods are well-known to those skilled in the art and are described in numerous publications. In addition, all the publications referred herein are integrated hereto as references.
EXAMPLES
Example 1
Preparation of pBacHTS
pBacHTS viral vectors were prepared. For the preparation, firstly, pBacPAK8_R1 (see FIG. 4) was provided by cloning amplified attR1 sites and Bsu36I recognition base sequences at BamHI/EcoRI sites of a shuttle vector of pBacPAK8 (Genebank: U2446, Clontech, California, U.S.A.) and transforming DH5α (Life Technologies Inc., Maryland, U.S.A.) with the cloned vector, and then by incubating and screening in agar medium including ampicillin. Likewise, pBacPAK8_R1R2 was prepared by cloning PCR amplified attR2 sites and Bsu36I recognition site sequences at EcoRI/PacI site sequences of pBacPAK8_R1 (see FIG. 5). In order to obtain pBacHTS, a DNA fragment (427 bp) including ccdB gene from EcoRI digested fragments of pEntr4 plasmid (Invitrogen, California, U.S.A.) was inserted to the pBacPAK8_R1R2, and then the resulting plasmid was transferred to DB3.1 cell (Life Technologies Inc., Maryland, U.S.A.). pBacHTS contained two different Bsu36I recognition sequences between the attR1 site and the attR2 site (FIG. 2). The attR1 sites and the attR2 sites included site-specific recombinase target sequences that reacted with attL1 and attL2 sites, respectively, in the presence of integrase from λ bacteriophage, Xis, IHF-α and IHF-β.
Example 2
Preparation of pBacHTS 6His, pBacHTS GST, pBacHTS HisGst, pBacHTS GFP and pBacHTS Flag
A fusion tag was inserted into the site in back of the polyhedrin promoter in order to prepare recombinant baculovirus expressing fusion proteins. pBacHTS_Gst was designed for the preparation of an expression vector for glutathione-s-transferase (GST) fusion protein. In order to accomplish this, pGEX-2T (Genbank: U13850) was PCR-amplified using a primer including Bg1II and a primer including BamHI linker, which in turn was treated with Bg1II and BamHI and then was inserted into pBacHTS/BamHI restriction sites. In addition, pBacHTS_His was designed for the preparation of a vector expressing His tag fusion protein by inserting 6 His linker to the BamHI site of pBacHTS. Furthermore, pBacHTS_HisGST was designed by inserting Bg1II-and-BamH1H-treated GST genes, which were PCR-amplified, to the BamHI site of pBacHTS_His. On the other hand, the green fluorescent protein (GFP) gene was PCR-amplified using a primer containing a BamHI linker and a primer containing a KpnI linker, which in turn was digested with BamHI/KpnI. After that, the digested gene was integrated into BamHI/KpnI restriction sites of pBacHTS to generate pBacHTS_GFP. Furthermore, pBacHTS Flag was prepared by inserting a linker expressing Flag tag at BamHI/KpnI sites of pBacHTS (see FIG. 7).
Example 3
Preparation of DNA of vBacHTS, vBacHTS His, vBacHTS HisGST and vBacHTS GFP Viruses
Baculoviruses of which polyhedrin loci were replaced by pBacHTS plasmids were prepared using homologous recombination. Briefly, Sf21 insect cells were transfected with a mixture of pBacHTS plasmid, Bsu36I digested BacPAK6 viral DNA (Clontech, California, U.S.A. #6144-1) and Lipofectin (Life Technologies Inc., Maryland, U.S.A.) to induce homologous recombination in the cells. The recombinant viruses were isolated through twice-repeated plaque assays, which in turn were subjected to PCR. The purified viral clone was named vBacHTS virus (SEQ. ID No. 1: the sequence of its polyhedrin locus) (see FIG. 15). As disclosed in FIG. 13, pBacHTS His (see FIG. 8), pBacHTS_HisGst (see FIG. 9), pBacHTS_GST and pBacHTS_GFP were respectively transferred together with the BacPAK6 virus to generate vBacHTS_His (SEQ. ID No. 2: the sequence of its polyhedrin locus), vBacHTS_HisGst (SEQ. ID No. 3: the sequences of its polyhedrin locus), vBacHTS_GST (SEQ. ID No. 4: the sequence of its polyhedrin locus) and vBacHTS_GFP (SEQ. ID No. 5: the sequence of its polyhedrin locus) (see FIG. 15). Viral plaques were selected from agarose medium.
Example 4
Purification of Viral DNA of vBacHTS, vBacHTS His, vBacHTS HisGst, vBacHTS GFP, and vBacHTS
Viral culture medium having 1.2×108 pfu/ml of viral titer was produced after 3 days from infecting Sf21 cells on a cell culture dish (100 mm diameter) in order to isolate vBacHTS viral DNA. Then, 1.25×107 of Sf21 cells were plated again on a cell culture dish (150 mm diameter), which in turn were infected with a 20 times larger number of viruses multiplicity of infection (MOI), i.e., MOI=20. After incubating for 48 hours, about 25 ml of cell culture medium per dish was obtained. A total of 150 ml of cell culture medium from 6 dishes (150 mm diameter) was centrifugated at 20,000 rpm for 90 minutes, and the resulting precipitated viral particles were recovered (with Hanil, Supra22k). The recovered viral particles were suspended in 2 ml of TE (10 mM Tris-HCl pH=8.0, 1 mM EDTA), and then were treated with a sucrose concentration gradient ultra-centrifuge (Beckman SW41 rotor) at 30,000 rpm. Viral particles were purified from the layer between 50% and 40% sucrose solution. The purified viruses were subjected to centrifugation again at 18,000 rpm for 90 minutes. After that, the precipitates of viral particles were suspended again with 2 ml of TE (10 mM Tris-HCl pH=8.0, 1 mM EDTA), and were left at 42° C. for 2 hours after adding 0.5% SDS, 1% beta-mercaptoethanol and 0.2 mg of Proteinase K thereto, so as to isolate viral envelopes. The viral lysate was extracted twice with the same amount of phenol/chloroform solution, and ethanol was added to the extract, resulting in pure viral DNA obtained as precipitates. Then, 50 units of the restriction enzyme Bsu361 (from New England Biolabs, Inc., Massachusetts, U.S.A., NEB #524) were added to the purified DNA (10 μg). The mixture was left at 37° C. for 2 hours before used in the following studies (see FIG. 16).
Example 5
Preparation of Gene Cassette
A pEntr_GFP gene cassette was prepared by inserting PCR products of GFP between the attL1 site and the attL2 site. A pEntr_GUS gene cassette from LTI was employed.
Example 6
Preparation of the Desired Recombinant Viruses Having GFP Gene or GUS Gene
Recombinant viruses expressing GFP and GUS were generated in this study. The pEntr_GFP gene cassette (100 ng) or the pEntr_GUS gene cassette (100 ng) was transferred to a test-tube, and reacted with 100 ng of Bsu36I treated vBacHTS viral DNA at 25° C. for 2 hours, in the presence of integrase mixture comprising 4 μl of integrase, Xis, IHF-α and IHF-β. Then, Sf21 cells were infected with the reaction mixture together with lipofectin (Life Technologies, Inc., Maryland, U.S.A.), thereby recombinant viruses were generated. After 2 days, green fluorescence was observed from the insect cells including the GFP gene cassette. Furthermore, after 4 days, almost every cell showed green fluorescence. Furthermore, fluorescence and symptoms of viral infection were observed in the infected cells.
On the other hand, a mixture containing the pEntr_GUS gene cassette was transferred to Sf21 cells. After 4 days, X-Gluc was added to the cells. After 2 hours of the reaction, the Sf21 cells became blue, which supported the expression of GUS (see FIG. 18). In order to determine the productivity of the recombinant viruses, a 4-day viral culture was dilated and transferred to insect cells. Next, plaques were detected 4 days after adding culture medium containing 1% low-melting point agarose to the infected cells. As the result, most plaques represented blue fluorescence (see FIG. 19).
Example 7
Determination of the Production Efficiency of Recombinant Viruses
Recombinant viruses expressing GFP were prepared in this study. In order to accomplish this, 100 ng of the pEntr_GFP gene cassette containing GFP genes and 200 ng of viral DNA of Bsu36I treated vBacHTS, vBacHTS_His or vBacHTS_HisGST were reacted in the presence of 4 μl of integrase mixture comprising integrase, Xis (excisionase), IHF-α and IHF-β at 25° C. for 6 hours. The resulting mixture was transferred to Sf21 cells together with lipofectin (Life Technologies, Inc., Maryland, U.S.A.) in order to generate recombinant baculoviruses. After incubating at 27° C. for 48 hours, the expression of GFP was detected under fluorescence microscope. Since the cells, in which baculoviruses replicated, represented fluorescence, the efficiency of recombinant viral expression was determined by counting the cells showing green fluorescence. In the meantime, BacPAK6 viral DNA (Clontech, California, U.S.A.) treated with Bsu36I and 500 ng of pBacPAK_GFP were transferred to Sf21 cells, then the expression of GFP in the Sf21 cells was monitored.







TABLE 3







The expression efficiency of GFP baculoviruses.










Virus DNA
Bsu36I
gene cassette
GFP positive cell#













BacPAK6
Yes
pBacPAK8 EGFP
154


VbacHTS

pEntr EGFP
1752


VbacHTS
yes
pEntr EGFP
572


VbacHTS His

pEntr EGFP
2236


VbacHTS His
yes
pEntr EGFP
654


VbacHTS HisGST

pEntr EGFP
1433


VbacHTS HisGST
yes
pEntr EGFP
475









As a result, the efficiency of viral expression is much higher in the method of the present invention compared to the prior art (see Table 3).
Example 8
Detection of the Efficiency of Recombinant Viral Expression
Recombinant viruses expressing GUS were prepared, and the number of plaques expressing GUS genes was counted. In order to accomplish this, firstly, 100 ng of the pEntr_GUS gene cassette containing GUS genes and 200 ng of each of the viral DNA of Bsu36I-treated vBacHTS, vBacHTS_His or vBacHTS_HisGST were reacted in the presence of 4 μl of integrase mixture comprising integrase, exisionase, IHF-α and IHF-β at 25° C. for 6 hours. The resulting mixture was transferred to Sf21 cells together with lipofectin (Life Technologies, Inc., Maryland, U.S.A.) to generate recombinant baculoviruses. Plaque assays were carried out for the viral culture medium. On the other hand, in order to detect productivity of the recombinant viruses, a 4-day viral culture medium was dilated and transferred to insect cells. Subsequently, the cells were incubated for 4 days after adding medium containing 1% low-melting point agarose thereto. The number of plaques expressing GUS genes were counted after 4 days visible from the addition of 100 μl of 0.33% neutral red water solution and 25 μl of X-Gluc (20 mg/ml in DMSO) and afer subsequent dye treatment (see Table 4).







TABLE 4







The efficiency of GUS recombinant viral expression.
















Recom-



Virus DNA
Bsu36I
gene cassette
Total
binant
rate %















BacPAK6
yes
pBacPAK8
46
41
89%




EGFP


VbacHTS

pEntr GUS
28
25
89%


VbacHTS
yes
pEntr GUS
57
57
100%


VbacHTS His

pEntr GUS
44
36
82%


VbacHTS His
yes
pEntr GUS
46
45
98%


VbacHTS HisGST

pEntr GUS
82
57
70%


VbacHTS HisGST
yes
pEntr GUS
32
32
100%


VbacHTS GFP

pEntr GUS
27
22
81%


VbacHTS GFP
yes
pEntr GUS
21
20
95%









As a result, most of the plaques represented blue color when they were treated with X-Gluc, which supported that the efficiency of GUS viral generation was very high in comparison to the prior art.
Example 9
High-Throughput Preparation of Recombinant Viruses in Multi-Well Plate
Desired recombinant viruses were prepared simultaneously from a multi-well plate. For this purpose, the vBacHTS viral DNA was treated with Bsu36I restriction enzyme. In this study, a GFP gene cassette was employed to confirm the generation of recombinant baculoviruses and gene expression. The GFP gene cassettes were incubated in a 96-deep well plate simultaneously and purified using an automatic device. All the processes were carried out in the multi-well plate. The recombination reaction, insect cell incubation, and viral infection were performed using an 8-channel pipette. About 50 ng of the gene cassette and 200 ng of vBacHTS baculoviral DNA were reacted in the presence of 2 μl of recombinase and 4 μl of buffer at 25° C. for 12 hours. A total of 20 pt of reaction mixture was used in this reaction. In order to detect the insertion of the gene cassette, PCR amplification was performed using primers for polyhedrin locus amplification.
Baculo-Forward primer: 5-actgttttcgtaacagttttg-3 (SEQ. ID No.: 6)
Baculo-Reverse primer: 5-acaacgcacagaatctagc-3 (SEQ. ID No.: 7)
As a result, recombinant viral DNA was generated with very high efficiency. Meanwhile, liposome was prepared by mixing 5 μl of the recombinant reaction mixture with 5 μl of 10% lipofectin dilates, which in turn was transfened to 50,000 of Sf21 cells in a 96-well plate (SPL) followed by the incubation of the cells for 4 days. Protein expression was assayed after a 3-day incubation of 50,000 of the Sf21 cells that were infected again with 10 μl of viruses. As for GFP viruses, the expression of green fluorescence was detected under the fluorescence microscope. And, the exhibition of symptoms of GFP viral infection was detected also. The cells were isolated from each of the wells with SDS-PAGE, and the expression of GFP was assayed using GFP-antibody with western blot. With regard to GFP proteins, the measured value showed a similar pattern as detected under the fluorescence microscope (see FIG. 22).
Example 10
High-Throughput Preparation and Enzyme Activity Screening of LacZ Gene Mutants in a 96-Well Plate Using GFP Recombinant Baculoviruses
In order to prepare desired recombinant baculoviruses (sized about 13.2 kb) from a multi-well plate simultaneously, the vBacHTS_GFP viral DNA was treated with Bsu36I restriction enzyme. Gene cassettes of pEntr_LacZdel were employed in this study. The gene cassettes were prepared in a 96-well plate by PCR cloning of the gene of β-galactosidase from E. coli (sized about 3.2 kb), wherein the gene was deleted at the 3′-terminus. More specifically, pEntr_LacZ was prepared by PCR cloning of the gene of LacZ. Afterward, pEntr_LacZ was treated with an ExoIII/S1 deletion kit (#K0421) (from Fermentas) to generate pEntr_LacZdel. All the processes were carried out in a multi-well plate. The recombination reaction, insect cell incubation and viral infection were performed with an 8-channel pipette. 50 ng of gene cassettes and 200 ng of vBacHTS baculoviral DNA was reacted in the presence of 2 μl of recombines and 4 μl of buffer at 25° C. for 12 hours. A total of 20 μl of reaction mixture was used in this reaction. In order to detect the insertion of the gene cassette, PCR amplification was performed using a pair of primers (Seq. ID No. 6 and Seq. ID No. 7) for the amplification of polyhedrin locus. As a result, recombinant viruses were generated at very high efficiency (see FIG. 25). Meanwhile, liposome was prepared by mixing 5 μl of the recombinant reaction mixture and 511 of 10% lipofectin dilates, which in turn was transferred to 50,000 of Sf21 cells in a 96-well plate (SPL) followed by incubation of the cells for 4 days (see FIG. 26). In order to assay the expression of GFP fusion proteins, SDS-PAGE analysis and western blotting using GFP antibodies were carried out (see FIG. 26).
In order to screen the gene activities, 1.5 μl of X-Gal (25 mg/ml in DMSO) of developer of β-galactosidase was added to each well that contained viruses incubated for 3 days after the primary infection. After 12 hrs of reaction, viruses containing β-galactosidase activity were detected in 2 (two) wells (see FIG. 27).
Example 11
High-Throughput Heterologous Gene Expression Using Recombinant Baculoviruses in a 96-Well Plate and the Screening of Enzyme Activity Using the Same
S. cerevisiae, which includes 124 protein kinase genes, was employed in this study. PCR amplification and cloning were carried out using gene-specific primers to obtain 112 gene cassettes from the S. cerevisiae genome. Recombinant baculoviruses were prepared by the recombination of the gene cassettes and the vBacHTS_GFP vector DNA. The respective recombinant viruses represented particular fluorescence according to the proteins fused to GFP (see FIG. 28). Also, the recombinant baculoviruses having 32 human cDNA were prepared in the same manner.
Firstly, cells were infected with these viruses and incubated for 3 days. The cell lysate was generated using a buffer to lyse cells. Viruses, which exhibited protein kinase activities to substrates of Histon H1, myelin basic protein (MBP) and Rb, were screened. 2 μg of protein substrates (histon H1, MBP and Rb) were reacted with 10 μl of cell extracts at 30° C. for 10 minutes, in the presence of 10 μM adenosine triphosphate (ATP), 0.2 uCi of P32-6-labeled ATP (gamma, P32 ATP), and 2 μl of phosphate buffer (200 mM Tris-HCl (pH=8.0), 100 mM of MgCl2, 10 mM of ethylene glycol tetraacetic acid (EGTA) and 10 mM of diothiothreitol (DTT)). After stopping the reaction by adding 120 μl of 1% phosphoric acid solution, the reaction mixture was transferred to a polyvinylidene difluoride (PVDF) membrane (Millipore, Massachusetts, U.S.A., #MAIP-N45). Afterwards, the membrane was washed with detergent (10 mM Tris-HCl (pH-8.0), 1 mM ethylenediamine tetraacetic acid (EDTA) and 150 mM NaCl) four times and dried, which in turn was exposed to phosphoscreen at room temperature. Signals were detected with a Phosphoimager (Molecular Dynamics, California, U.S.A or Fuji, BAS, Japan). As a result, it was observed that protein kinase activities were increased in some viruses (see FIG. 29). Subsequently, SDS-PAGE electophoretic analysis was carried out to confirm the specificity of protein phosphorylation. At that time, the level of Rb protein phosphorylation with regard to the concentration of protein kinase included in cell extracts was detected, while varying the concentrations of cell extracts. As a result, only the cell extracts of the baculoviruses expressing plate#2-D3 protein and plate#2-A9 protein increased Rb protein phosphorylation in a concentration-dependent manner (see FIG. 30). Meanwhile, proteins of plate#2-D1 and plate#2-D2 exhibited very weak phosphorylation activities. And, it was acknowledged that the positive signals from the proteins of plate#2-D1 and plate#2-D2 resulted from auto-phosphorylation activities rather than from Rb protein phosphorylation. Rb protein phosphorylations by plate#2-D3 and plate#2-A9 proteins exhibited a typical protein phosphorylation pattern in that phosphorylation of Rb protein was dependent on the concentration of the substrate and the enzyme (FIG. 31). Thus, it is possible to find out new useful proteins from baculoviral libraries obtained from the high-throughput system according to the present invention.
Example 12
The Preparation of pBacHTS2 and pBacHTS2 GFP
Baculoviral transfer vector of pBacHTS2 was prepared in order to generate vBacHTS2 viruses (SEQ. ID No. 8: the sequence of its polyhedrin locus) that can replicate and can be applied to a recombination reaction in vitro. The pBacHTS2 had a bacterial artificial chromosome (BAC) vector originated the replication origin and chloramphenichol resistance gene (CmR) at the Bsu36I restriction enzyme recognition site located between the attR1 site and the attR2 site thereof. Thus, it was the type of BAC vector that can replicate in bacteria. Replacing the BAC vector originated replication origin and CmR with the desired gene cassette generated vBacHTS viruses in vitro.
In order to prepare pBacHTS2, firstly, 6.5 kb of DNA fragment containing the BAC vector replication origin and CmR was generated using pBACe3.6 (Genbank: U80929) as a template. Then, PCR amplification was carried out using 10 μmol of a pair of sequences having Bsu36I recognition sequences, 200 μM of dNTPs and 2.5 μl of PfuTurbo polymerase (Stratagene) with PCR cycler (Applied Biosystems, California, U.S.A., Gene Amp PCR System 2700). A total of 50 μl of reaction mixture was used. PCR was carried out for 20 cycles (DNA denaturation at 95° C., 30 seconds, DNA extension at 60° C., 30 seconds, DNA amplification at 72° C., 7 minutes). PCR products of 6.5 kb of DNA fragment and vBacHTS vector were digested by Bsu36I, and were reacted in the presence of T4 ligase at 16° C. overnight. E. coli (DH5a) was transformed using the resulting mixture, which in turn was incubated with Cland Amp medium (for selection) to produce pBacHTS2. Likewise, Bsu36I treated PCR products of 6.5 kb of DNA fragment were inserted to Bsu36I site of the pBacHTS_GFP vector so as to obtain pBacHTS2_GFP vector.
Example 13
Preparation of Viruses Having Site-Specific Recombination Sites
Baculoviruses were prepared using homologous recombination, which replicated in bacteria. Briefly, the homologous recombination was induced in St21 cells by transferring a mixture of pBacHTS2 plasmid, Bsu36I digested BacPAK6 DNA and Lipofectin (Life Technologies, Inc., Maryland, U.S.A.). The infected cells were incubated at 27° C. for 4 days, and were transferred to 5×106 of Sf21 cells (in 100 mm dish). Thereby, high titer of viruses was obtained. Then, precipitates of viral particles were produced by centrifugation after adding 2 ml of 50% PEG6000 to the cell culture medium. Next, proteinase K was added to the mixture at 42° C. and left alone for 2 hours to dismantle the viral envelope. The viral lysate was extracted twice using the same amount of phenol/chloroform, and ethanol was added thereto. Thereby, precipitated and purified vBacHTS2 viral DNA (SEQ. ID No. 8: the sequence of its polyhedrin locus) were obtained. Then, cell lines (Life Technologies, Inc., Maryland, U.S.A.) were transformed with the purified DNA using MicroPulser (Bio-Rad, California, U.S.A.), which are in turn incubated in Cm medium to form a bacterial colony. The bacteria were incubated in 1 liter of 2xYT medium (10 g of Yeast extract powder, 16 g of tryptone, 5 g of NaCl within per liter), then DNA was purified and named as bBacHTS2 (FIG. 16). Thus, according to this method, it is possible to reduce the required time-period and cost significantly, since the viral DNA can be obtained from bacterial culture without the need of incubation in insect cells. Purified 10 μg of DNA was digested with 50 units of Bsu36I at 37° C. for 5 hours, which in turn was heat treated at 80° C. for 20 minutes to inactivate Bsu361 enzyme. Likewise, vBacHTS2_GFP (SEQ. ID No. 9) was prepared from pBacHTS2_GFP vector by homologous recombination; and then was transferred to DH10B by electrophoration. The DNA was purified and named as bBacHTS2_GFP (see FIG. 16).
Example 14
Preparation of the Desired Recombinant Viruses Using vBacHTS2 and vBacHTS2 GFP DNA Generated from Bacteria
50 ng of the pEntr_GFP and the pEntr_GUS gene cassettes were reacted with 200 ng of Bsu36I treated vBacHTS2 viral DNA in the presence of 1 μl of integrase mixture in vitro at 25° C. for 12 hours. The same reaction was carried out except for the use of the pEntr_GUS gene cassette in place of the pEntr_GFP gene cassette. PCR was performed as disclosed in the Examples mentioned above. PCR amplification was carried out using the reaction mixture, as templates, and a pair of primers amplifying the viral polyhedrin locus to confirm whether a recombination reaction occurred. A total of 20 cycles of PCR were carried out using each of 10 pmole of the primers and 1 tube of Bioneer premix kit, in which one cycle of PCR was performed at 95° C. for 30 seconds, 50° C. for 30 seconds and 72° C. for 3 minutes. After completing PCR reaction, electrophoresis was carried out for the PCR products on 1% agarose gel to confirm efficient performance of recombination. The gene cassette reaction mixture was transferred to Sf21 cells together with 5 μl of Lipofectin (Life Technologies, Inc., Maryland, U.S.A.) so as to obtain baculoviruses.
Green fluorescence was observed in insect cells, after 2 days from transferring GFP gene cassette reaction mixture thereto. In addition, most of the cells represented green fluorescence after 4 days from transfer (see FIG. 25). Sf21 cells were infected again with the viral culture medium to confirm green fluorescence and the symptoms of infection. Likewise, pEntr_GUS gene cassette was reacted with Bsu36I treated vBacHTS2 DNA at 25° C. for 12 hours. Then, the obtained reaction mixture was transferred to Sf21 cells and was incubated at 27° C. for 4 days. When 6 μl of X-Gluc (20 mg/ml in DMSO) was added to incubated cells, all the culture medium represented a strong blue color, which supported not only the expression of GUS genes but also efficient generation of recombinant viruses containing GUS genes.

## Claims

1. A method for preparing expressive circular recombinant viral vectors, comprising:
i) providing a plurality of linearized viral DNA fragments wherein each fragment contains at least two site-specific recombination sites and at least one restriction enzyme recognition site;
ii) providing a plurality of viral vector carriers wherein each viral vector carrier contains a gene cassette having a desired genomic material with a desired nucleic acid sequence flanked with at least two site-specific sites for homologous recombination with the linearized DNA fragments at the two site-specific recombination sites; and
iii) reacting the linearized viral DNA fragments and the viral vector carriers to create homologous recombinations in vitro wherein a plurality of recombinant viral vectors carrying the desired genomic material is formed in vitro therefrom;
iv) wherein non-recombined linearized viral DNA fragments, non-recombined viral vector carriers, and non-linearized viral DNA do not express a gene for a protein responsible for viral replication and viral particle formation.

2. The method for preparing expressive circular recombinant viral vectors as claimed in claim 1, wherein one or more viral DNA fragments are digested with restriction enzymes at one or more sites to generate the linearized viral DNA fragments.

3. The method for preparing expressive circular recombinant viral vectors as claimed in claim 1, wherein the recombinant viral vectors are obtained from the group consisting of baculovirus, poliomavirus, papillomavirus, and hepatitis B virus (HBV).

4. The method for preparing expressive circular recombinant viral vectors as claimed in claim 2, wherein said one or more sites comprise the nucleotide sequence of CCTNAGG.

5. A method of preparing recombinant viruses having circular genomic DNA, comprising:
i) providing a plurality of linearized viral DNA fragments wherein each fragment contains at least two site-specific recombination sites and at least one restriction enzyme recognition site;
ii) providing a plurality of viral vector carriers wherein each viral vector carrier contains a gene cassette having a desired genomic material with a desired nucleic acid sequence flanked with at least two site-specific sites for homologous recombination with the linearized DNA fragments at the two site-specific recombination sites; and
iii) reacting the linearized viral DNA fragments and the viral vector carriers to create homologous recombinations in vitro to produce a reaction mixture including expressive circular recombinant viral vectors carrying the desired genomic material formed in vitro therefrom;
iv) wherein non-recombined linearized viral DNA fragments, non-recombined viral vector carriers and non-linearized viral DNA do not express a gene for a protein responsible for viral replication and viral particle formation; and
v) transferring the reaction mixture to host cells in a multi-well plate.

6. The method of preparing recombinant viruses having circular genomic DNA as claimed in claim 5, wherein the transfer of the reaction mixture to host cells is carried out without a need for a selection process to isolate the circular genomic DNA.

7. The method of preparing recombinant viruses having circular genomic DNA as claimed in claim 5, wherein viral genomic DNA of i) are digested with a restriction enzyme at one or more sites to generate the linearized viral DNA fragments.

8. The method of preparing recombinant viruses having circular genomic DNA as claimed in claim 5, wherein the recombinant viral vectors are obtained from the group consisting of baculovirus, poliomavirus, papillomavirus, and hepatitis B virus (HBV).

9. The method of preparing recombinant viruses having circular genomic DNA as claimed in claim 7, wherein said one or more sites comprise the nucleotide sequence of CCTNAGG.