Abstract: Recombinational cloning is provided by the use of nucleic acids, vectors and methods, in vitro and in vivo, for moving or exchanging segments of DNA molecules using engineered recombination sites and recombination proteins to provide chimeric DNA molecules that have the desired characteristic(s) and/or DNA segment(s).

Abstract: The present invention provides compositions, methods, and kits for covalently linking nucleic acid molecules. The methods include a strand invasion step, and the compositions and kits are useful for performing such methods. For example, a method of covalently linking double stranded (ds) nucleic acid molecules can include contacting a first ds nucleic acid molecule, which has a topoisomerase linked to a 3? terminus of one end and has a single stranded 5? overhang at the same end, with a second ds nucleic acid molecule having a blunt end, such that the 5? overhang can hybridize to a complementary sequence of the blunt end of the second nucleic acid molecule, and the topoisomerase can covalently link the ds nucleic acid molecules. The methods are simpler and more efficient than previous methods for covalently linking nucleic acid sequences, and the compositions and kits facilitate practicing the methods, including methods of directionally linking two or more ds nucleic acid molecules.

Abstract: The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

Abstract: The present invention relates to the generation of replication-competent viruses having therapeutic utility. The replication-competent viruses of the invention can express proteins useful in the treatment of disease.

Abstract: The present invention relates to methods of developing gene inserts that are more compatible with the host vectors by modifying a protein sequence to lessen potential interference with vector propagation while ensuring that the protein is expressed and processed efficiently and maintains desired structural features, and designing a gene with a nucleotide sequence that resembles the base composition of the host vector genome.

Abstract: SARS (severe acute respiratory syndrome virus, a coronavirus) immunogens, antigens, or epitopes, nucleic acid molecules encoding such immunogens, antigens, or epitopes; vectors containing such nucleic acid molecules, e.g., viral vectors such as baculovirus vectors, DNA vectors, such as DNA plasmid vectors, e.g., DNA plasmids that express a nucleic acid molecule in a mammalian cell, uses for such immunogens, antigens or epitopes and vectors, e.g., as an active component immunogenic, immunological or vaccine compositions, or to generate antibodies, such as monoclonal antibodies, and methods for making, and using such immunogens, antigens or epitopes, vectors, antibodies, including in methods for eliciting an immunological or immunogenic or vaccine response, as well as in assays or diagnostic kits or methods, are discussed, as well as a seamless fusion of sequences in a plasmid or vector, e.g., a sequence encoding a leader sequence and a sequence encoding a protein, epitope or immunogen or antigen.

Abstract: Methods of assembling modified adenoviruses, libraries of adenoviral gene modules and compositions thereof are provided herein.

Abstract: SARS (severe acute respiratory syndrome virus, a coronavirus) immunogens, antigens, or epitopes, nucleic acid molecules encoding such immunogens, antigens, or epitopes; vectors containing such nucleic acid molecules, e.g., viral vectors such as baculovirus vectors, DNA vectors, such as DNA plasmid vectors, e.g., DNA plasmids that express a nucleic acid molecule in a mammalian cell, uses for such immunogens, antigens or epitopes and vectors, e.g., as an active component immunogenic, immunological or vaccine compositions, or to generate antibodies, such as monoclonal antibodies, and methods for making, and using such immunogens, antigens or epitopes, vectors, antibodies, including in methods for eliciting an immunological or immunogenic or vaccine response, as well as in assays or diagnostic kits or methods, are discussed, as well as a seamless fusion of sequences in a plasmid or vector, e.g., a sequence encoding a leader sequence and a sequence encoding a protein, epitope or immunogen or antigen.

Abstract: A method for performing homologous recombination between at least a first nucleic acid molecule and a second nucleic acid molecule which share at least one region of sequence homology. A method for improving the efficiency of homologous recombination.

Abstract: The present disclosure relates to protein and nucleic acid mutants of chondroitinase ABCI. Such nucleic acid mutants encode for chondroitinase ABCI mutant enzymes exhibiting altered chondroitin lyase activity or increased resistance to inactivation from stressors including UV light or heat. Methods of using such nucleic acid mutants encoding chondroitinase ABCI mutant enzymes is also provided.

Abstract: There is provided a method for inserting a nucleic acid sequence that encodes a foreign peptide into a poxvirus genome, said method comprising: identifying in the poxvirus genome a poxvirus open reading frame wherein said open reading frame is characterised by an initial ATG start codon and wherein expression of said open reading frame is driven by an operably-linked poxvirus promoter located upstream of the open reading frame and wherein expression of said open reading frame provides a peptide that is non-essential to viability of the poxvirus; and inserting the nucleic acid sequence that encodes the foreign peptide at a position downstream of the poxvirus promoter; wherein following said insertion, (i) the nucleic acid that encodes the foreign peptide is operably-linked to the poxvirus promoter and expression of said nucleic acid is driven by said poxvirus promoter; and (ii) translation of the foreign peptide is initiated at an ATG start codon located at the same position as the ATG start codon of the poxvi

Abstract: Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.

Abstract: The invention provides molecular switches which couple external signals to functionality and to methods of making and using the same. The switches according to the invention can be used, for example, to regulate gene transcription, target drug delivery to specific cells, transport drugs intracellularly, control drug release, provide conditionally active proteins, perform metabolic engineering, and modulate cell signaling pathways. Libraries comprising the switches and expression vectors and host cells for expressing the switches are also provided.

Abstract: Biosensors, compositions comprising biosensors, methods of producing biosensors, and methods of using biosensors are disclosed. The biosensors comprise a fluorogen-activating peptide and a blocking peptide. The fluorogen-activating peptide and blocking peptide are covalently linked through a peptide linker. The blocking peptide associates with the fluorogen-activating peptide thereby blocking an active domain of the fluorogen-activating peptide when the linker is in an unmodified state. The peptide linker may contain an amino acid sequence that is specifically recognized as a modification substrate by a cognate enzyme. The fluorogen-activating peptide and the blocking peptide at least partially disassociate when the linker is modified by an enzyme, thereby allowing the fluorogen-activating peptide to bind a cognate fluorogen and modulate a fluorescence signal.

Abstract: A method of producing a selectable marker gene-free plasmid by culturing a plasmid containing a selectable marker gene flanked by site specific recombinase target sites in a host cell environment incapable of effecting recombination between the site specific recombinase target sites and subsequently culturing the plasmid in another host cell environment which is capable of effecting recombination between the site specific recombinase target sites, so that the selectable marker gene is excised. Uses of plasmids produced by the method for the production of recombinant protein for therapeutic and vaccine purposes, production of therapeutic DNA and DNA vaccines and delivery of recombinant protein and DNA to a patient using live bacterial vectors.

Abstract: The invention provides molecular switches which couple external signals to functionality, and combinatorial methods of making and using the same involving circular permutation of nucleic acid and amino acid sequences. The switches according to the invention can be used, for example, to regulate gene transcription, target drug delivery to specific cells, transport drugs intracellularly, control drug release, provide conditionally active proteins, perform metabolic engineering, and modulate cell signaling pathways. Libraries comprising the switches, expression vectors and host cells for expressing the switches are also provided.

Abstract: Embodiments of the present invention generally disclose methods, compositions and uses for generating and expressing poxvirus constructs. In some embodiments, constructs may contain an influenza virus gene segment. In certain embodiments, methods generally relate to making and using compositions of constructs including, but not limited to, poxvirus vaccine compositions. In other embodiments, vaccine compositions are reported of use in a subject.

Abstract: The invention concerns a recombinant vector characterized in that it comprises a polynucleotide comprising a central initiation cis-active region (cPPT) and a termination cis-active region (CTS), the regions being of retroviral or retroviral-like origin, and the vector further comprising a predetermined nucleotide sequence (transgene or nucleotide sequence of interest) and retrotranscription regulating, expressing, and packaging signals of retroviral or retroviral-like origin.

Abstract: The present invention relates to a polypeptide, described as a lectin, its encoding nucleic acid sequence and antibodies to the polypeptide and their use in various medical applications, particularly for treating or preventing an autoimmune disorder, an inflammatory disorder or damaged skin in an animal.

Abstract: A genetically engineered strain WSJ-IA for producing isovaleryl spiramycin I. Also provided is a method for preparing the strain, comprising the steps of: (a) constructing a recombinant plasmid comprising a double gene ist-acyB2; (b) transforming the plasmid into an isovaleryl spiramycin I—producing strain to obtain the strain WSJ-IA. The level of isovaleryl spiramycin I produced by fermentation of the strain WSJ-IA is increased 1.7 times and the fermentation potency thereof increased 4.14 times in comparison with the strain exclusively comprising a single gene ist.

Abstract: The present invention is related to integrated method and tools to construct recombinant DNA molecules (to be used as DNA vaccine or gene therapy) without requiring the use of antibiotic(s) resistance gene(s) and without requiring the addition of one or more antibiotic(s) to the culture medium of cells submitted to this recombinant DNA method. The present invention allows to obtain the selection of recombinant host cell(s) transformed by a (exogenous) nucleic acid sequence of interest (extra-chromosomal vector containing the insert) and simultaneously stabilization (stable inheritance) of this (exogenous) nucleic acid sequence of interest into the transformed host cell(s) descendants (maintenance of the nucleic acid sequence of interest in the host cells population).

Abstract: An objective of the present invention is to provide methods for introducing DNAs encoding a desired amino acid sequence into a region comprising a DNA encoding an antibody variable region of antibody-producing cells. The present inventors developed methods for efficiently introducing DNAs encoding a desired amino acid sequence into the antibody variable region gene locus of DT40-SW, which is a mutant line of the DT40 chicken B cell line which has the ability to spontaneously introduce mutations. This allows mutagenesis of introduced DNAs to modify the polypeptides to have superior functions. In particular, the present inventors revealed the nucleotide sequence of the antibody H chain variable region gene locus of the DT40 cell line. Based on this finding, the present inventors successfully constructed targeting vectors that allow efficient substitution of the antibody H chain variable region gene locus of the DT40 cell line with a gene encoding a desired polypeptide.

Abstract: Methods are disclosed for assembling a plurality of double-stranded DNA fragments into DNA molecules in a single in vitro recombination reaction comprising contacting the plurality of double-stranded DNA fragments with a bacterial extract derived from a RecA deficient bacterial strain so as to assemble the plurality of DNA fragments into DNA molecules.

Abstract: Embodiments herein report compositions, systems and methods for making and using plasmid vectors and nanotube complexes. In certain embodiments, compositions, systems and methods herein include making plasmid vectors having aptamer inserts. In some embodiments, methods disclosed herein may be used to rapidly generate large quantities of plasmid vectors having aptamer inserts directed to a particular target agent. Other aspects concern plasmid constructs associated with organic semiconductors. Yet other aspects concern complexes of nanotubes associated with dsDNA aptamers and tracking molecules.

Abstract: The present invention provides minicircle nucleic acid vector formulations for use in administering to a subject, wherein the minicircle nucleic acid vectors include a polynucleotide of interest, a product hybrid sequence of a unidirectional site-specific recombinase, and are devoid of plasmid backbone bacterial DNA sequences. Also provided are methods of producing the subject formulations as well as methods for administering the minicircle nucleic acid vector formulations to a subject. The subject methods and compositions find use in a variety of different applications, including both research and therapeutic applications.

Abstract: The present invention provides duplexed parvovirus vector genomes that are capable under appropriate conditions of forming a double-stranded molecule by intrastrand base-pairing. Also provided are duplexed parvovirus particles comprising the vector genome. Further disclosed are templates and methods for producing the duplexed vector genomes and duplexed parvovirus particles of the invention. Methods of administering these reagents to a cell or subject are also described. Preferably, the parvovirus capsid is an AAV capsid. It is further preferred that the vector genome comprises AAV terminal repeat sequences.

Abstract: Provided is a method for selectively obtaining, for a given target gene, a “joined DNA fragment” wherein just a target gene fragment is joined with desired other DNA fragments, regardless of whether a DNA fragment containing a target gene sequence has been purified. In the provided method, a double-stranded joining DNA fragment containing a sequence A and/or a sequence B is selectively joined to the ends of a target gene fragment. A mixture of a double-stranded gene fragment, the 3? end of which is protruding, and the double-stranded joining DNA fragment, which are related in a prescribed manner, undergoes at least two cycles of thermal denaturation, reassociation, and DNA synthesis, resulting in a “joined DNA fragment,” which is a double-stranded DNA fragment including at least one instance of a sequence resulting from joining sequence A, the target gene sequence, and sequence B. A “single-side joined DNA fragment” can also be obtained, by a similar method.

Abstract: Methods are provided for producing a vector that includes at least one spliceable intron. In the subject methods, intron containing vectors are produced from donor and acceptor vectors that each include a site specific recombinase site, where the subject donor and acceptor vectors further include splice donor and acceptor sites that, upon site specific recombination of the donor and acceptor vectors, define an intron in the product vector of the recombination step. Also provided are compositions for use in practicing the subject methods, including the donor and acceptor vectors themselves, as well as systems and kits that include the same. The subject invention finds use in a variety of different applications, including the production of expression vectors that encode C-terminal tagged fusion proteins, the production of expression vectors that encode pure protein and not a fusion thereof, and the like.

Abstract: Targeting constructs and methods of using them are provided for differentiation-dependent modification of nucleic acid sequences in cells and in non-human animals. Targeting constructs comprising a promoter operably linked to a recombinase are provided, wherein the promoter drives transcription of the recombinase in an differentiated cell but not an undifferentiated cell. Promoters include Blimp1, Prm1, Gata6, Gata4, Igf2, Lhx2, Lhx5, and Pax3. Targeting constructs with a cassette flanked on both sides by recombinase sites can be removed using a recombinase gene operably linked to a 3?-UTR that comprises a recognition site for an miRNA that is transcribed in undifferentiated cells but not in differentiated cells. The constructs may be included in targeting vectors, and can be used to automatically modify or excise a selection cassette from an ES cell, a non-human embryo, or a non-human animal.

Abstract: The present invention provides compositions and methods for recombinational cloning. The compositions include vectors having multiple recombination sites and/or multiple topoisomerase recognition sites. The methods permit the simultaneous cloning of two or more different nucleic acid molecules. In some embodiments the molecules are fused together while in other embodiments the molecules are inserted into distinct sites in a vector. The invention also generally provides for linking or joining through recombination a number of molecules and/or compounds (e.g., chemical compounds, drugs, proteins or peptides, lipids, nucleic acids, carbohydrates, etc.) which may be the same or different.

Abstract: A gene construct comprising a programmed-cell-death executioner gene having a nuclear localization signal, a deleted signal peptide, an inhibitor-resistant binding site, a promoter, and an activator. A method of making a gene construct, by modifying a programmed-cell-death executioner gene by adding a nuclear localization signal, deleting a signal peptide, mutating a binding site for an inhibitor to make it inhibitor-resistant, adding a promoter for exclusive expression in selected cells, and adding an activator. A method of eliminating undesired cells from a patient. A method of treating cancer. An array comprising at least two gene constructs wherein all of the gene constructs differ with respect to the programmed-cell-death executioner gene and the nuclear localization signal. A method of personalizing anti-cancer treatment. A method of increasing DNase 1 resistance to actin binding. A method of increasing catalytic activity of DNase 1 binding.

Abstract: The invention provides molecular switches which couple external signals to functionality, and combinatorial methods of making and using the same involving circular permutation of nucleic acid and amino acid sequences. The switches according to the invention can be used, for example, to regulate gene transcription, target drug delivery to specific cells, transport drugs intracellularly, control drug release, provide conditionally active proteins, perform metabolic engineering, and modulate cell signaling pathways. Libraries comprising the switches, expression vectors and host cells for expressing the switches are also provided.

Abstract: The present invention relates to a method for isolating from the immunological gene repertoire a gene coding for a receptor having the ability to bind a preselected ligand. Receptors produced by the gene isolated by the method, particularly catalytic receptors, are also contemplated.

Abstract: A recombinant antibody vector for producing a single chain recombinant antibody comprises: (a) a contiguous nucleotide sequence: (i) that comprises a restriction endonuclease site that encodes an amino acid sequence of an immunoglobulin variable region; and (ii) that encodes an immunoglobulin constant region amino acid sequence in the same reading frame as (i), wherein another nucleotide sequence encoding (iii) an immunoglobulin variable region amino acid sequence, is insertable into the restriction endonuclease site in the same reading frame as (ii); and (b) one or more regulatory nucleotide sequences operably linked or connected to said nucleotide sequence, wherein the amino acid sequence in (i) comprises amino acids conserved in different immunoglobulin variable regions. The restriction endonuclease site may be a SacI site which encodes the conserved amino acids glutamate and leucine. In frame insertion of the nucleotide sequence of (iii) is facilitated by ligase independent cloning.

Abstract: The invention provides vectors and methods for directional cloning.

Abstract: This invention provides methods and compositions for assembling biological constructs (e.g., plasmids, transformed cells, etc.). In certain embodiments the methods involve encapsulating separate components of said biological construct each in a fluid droplet confined in a fluid channel; optionally mixing droplets from different fluid channels to for a sequenced order of droplets carrying different components of said biological construct in a channel or chamber; and optionally combining two or more droplets each containing different components of said biological construct to permit said components to react with each other in one or more reactions contributing to the assembly of said biological construct.

Abstract: The present invention provides a 2 ?m-family plasmid comprising a polynucleotide sequence insertion, deletion and/or substitution between the first base after the last functional codon of at least one of either a REP2 gene or an FLP gene and the last base before the FRT site in an inverted repeat adjacent to said gene.

Abstract: According to the present invention, a DNA construct of interest is assembled from overlapping subfragments via an acceptor module which comprises the distal end of the construct at a position downstream from a promoter. The construct is assembled distal to proximal via homologous recombination events occurring in the span between that distal end of the construct and the upstream end of the promoter. These recombination events occur iteratively between the acceptor module and alternative donor modules. Successful recombination places one of at least two marker genes under the transcriptional control of an active form of the promoter. As a result of alternating use of two varieties of donor modules, as few as two selection markers may be used to produce a complex DNA construct.

Abstract: A method for designing a bi-shRNA expression cassette encoding a bi-shRNA comprising: selecting one or more target site sequences; providing a backbone sequence comprising a first and a second stem-loop structure, inserting a first passenger strand and a second passenger strand and providing for synthesis of the bi-shRNA expression cassette.

Abstract: An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5?-terminus sequence and the second tag comprises the 3?-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.

Abstract: The present invention relates to a nucleic acid containing at least one homing endonuclease site (HE) and at least one restriction enzyme site (X) wherein the HE and X sites are selected such that HE and X result in compatible cohesive ends when cut by the homing endonuclease and restriction enzyme, respectively, and the ligation product of HE and X cohesive ends can neither be cleaved by the homing endonuclease nor by the restriction enzyme. Further subject-matter of the present invention relates to a vector comprising the nucleic acid of the present invention, host cells containing the nucleic acid and/or the vector, a kit for cloning and/or expression of multiprotein complexes making use of the vector and the host cells, a method for producing a vector containing multiple expression cassettes, and a method for producing multiprotein complexes.

Abstract: The present invention is in the fields of biotechnology and molecular biology. More particularly, the present invention relates to cloning or subcloning one or more nucleic acid molecules comprising one or more type IIs restriction enzyme recognition sites. The present invention also embodies cloning such nucleic acid molecules using recombinational cloning methods such as those employing recombination sites and recombination proteins. The present invention also relates to nucleic acid molecules (including RNA and iRNA), as well as proteins, expressed from host cells produced using the methods of the present invention.

Abstract: The present invention provides compositions, methods, and kits for covalently linking nucleic acid molecules. The methods include a strand invasion step, and the compositions and kits are useful for performing such methods. For example, a method of covalently linking double stranded (ds) nucleic acid molecules can include contacting a first ds nucleic acid molecule, which has a topoisomerase linked to a 3? terminus of one end and has a single stranded 5? overhang at the same end, with a second ds nucleic acid molecule having a blunt end, such that the 5? overhang can hybridize to a complementary sequence of the blunt end of the second nucleic acid molecule, and the topoisomerase can covalently link the ds nucleic acid molecules. The methods are simpler and more efficient than previous methods for covalently linking nucleic acid sequences.

Abstract: Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

Abstract: It is intended to provide a drug to be used in gene therapy which specifically targets abnormal cells such as tumor cells and destroys the same for healing. Namely, a drug comprising, as the active ingredient, a proliferative vector which contains a Survivin promoter proliferating depending on the expression of Survivin. This drug may be used in order to treat tumor. In this drug, use may be made of an adenovirus as the vector. In the adenovirus of this drug, an endogenous promoter of an E1A domain may be substituted with a Survivin promoter.

Abstract: Oncolytic human adenoviral vectors and cells and pharmaceutical compositions including the vectors. Also provided are methods for using the vectors in the manufacture of a medicament for treating cancer in a subject and a method of treating cancer in a subject. Furthermore, methods of producing an adenoviral vector are provided.

Abstract: Artificial chromosomes, including ACes, that have been engineered to contain available sites for site-specific, recombination-directed integration of DNA of interest are provided. These artificial chromosomes provide tractable, efficient and rational engineering of the chromosome for a variety of applications.

Abstract: The invention concerns a non-integrative and non-replicative recombinant lentivirus as well as its uses, in particular for preparing a composition for transferring genes in vitro, ex vivo or in vivo. The invention is useful for transferring genes in any mammal organism, for example in liver, muscle, pancreas or central nervous system (including the ocular sphere) tissues or cells, and in particular for treating disorders or pathologies such as, for example, central nervous system, including the ocular sphere, disorders.

Abstract: The present invention relates to a linker or population of linkers that include an oligonucleotide fixed portion and an oligonucleotide variable portion represented by formula (N)n, wherein N is A, C, G, T or U, or their derivatives, and n is an integer equal to or higher than 1. A linker-polynucleotide or a population of linker-polynucleotides of the invention may be constituted by said linker or population of linkers and a target first strand polynucleotide bound to said linker. The invention also encompasses a method of preparing said linker or population of linkers and a method of preparing a linker-polynucleotide using said linker or population of linkers. The linkers or polynucleotide-linkers of the invention can be used in a method of preparing a cDNA library.

Abstract: The present invention provides compositions, including vectors, and methods for the rapid subcloning of nucleic acid sequences in vivo and in vitro. In particular, the invention provides vectors used to contain a gene of interest that comprise a sequence-specific recombinase target site. These vectors are used to rapidly transfer the gene or genes of interest into any vector that contains a sequence-specific recombinase target site located downstream of a regulatory element so that the gene of interest may be regulated.