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G1236 Phdadshuttle6 G1236 pHDAdShuttle6 Map of Construct: Sequence of Construct: 2553bp LacZa (for blue/white bacterial screening)- 146-499 MCS- 396-482 3’-Overhang- 637-680 Ori- 805-1393 5’overhang- 1439-1486 Amp resistance (complementary)- 1493-2353 Amp promoter BsiWI sites-CGTACG TCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACA GCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGG CGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATA TGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCATTCGCCA TTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCT GGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCAC GACGTTGTAAAACGACGGCCAGTGAATTCCCTGCAGGACGCGTGGTACCAGGGGATCCACTA GTTCTAGAGTCGACGGCATGCAAGCTTAGCGGCCGCGATATCAGATCTGGCGTAATCATGGT CATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGA AGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCG CTCACTGCCCGCTTTCCCTACCAGTAAAAAAGAAAACCTATTAAAAAAACACCACTCGACGT ACGATGAACGGTCTCTACGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAA CATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTT TCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAA ACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTG TTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTT CTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGT GTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCC AACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGC GAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAA GAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGC TCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGAT TACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTACGGGGTCTGACGCGAACTGCCGATA CCTCGTACGTGGAAAAAATCAACAAAGGGATCCCCCGGGCTGCAGGAATTCGATGGAGACAG TTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAG TTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGT GCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCA GCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAA TTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCA TTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCC CAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGG TCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCAC TGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCA ACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACG GGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGG GGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCA CCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAG GCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCC TTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGA ATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTG ACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCC TTTCGTC Confirmation Digest: Information and Cloning Suggestions for Working with pHDAdShuttle: Background: Adenoviruses are very important tools in basic research. They are used to identify a proteins role in different biological processes both in vivo and in vitro. Adenoviral vectors were first generated by deleting portions of the E1 and E3 genes. Helper dependent or “gutless” adenoviral vectors have been generated as the final generation of adenoviral vectors. Helper dependent adenoviral vectors have had all expressed viral proteins removed. The viral “genome” only contains the adenoviral packaging signal, an untranslated portion of the E4 gene, and stuffer sequences. The pHDAdShuttle is a simple plasmid to prepare a gene cassette for insertion into one of the helper dependent adenoviral backbones. The final viral backbone with gene cassette that will be used for viral construction should be between 28kbp and 38kbp, so there are different empty backbone plasmids to choose from. Backbone Insert size available pΔ28E4 0-9kb pΔ25E4 3-12kb pΔ21E4 7-16kb pΔ17E4 11-20kb pΔ12E4 16-25kb pΔ8E4 20-29kb Helper Dependent Adenoviral Vectors Characteristics: • Episomal gene expression. • Infects dividing and non-dividing cells. • Transient high-level protein expression. • Accommodates inserts of up to 30kb. • Preps are produced with a titer of: 1E+10 to 5E+10 IGU/ml. (infectious genome units per ml). • Limited host immune response based on the lack of viral protein products. Disadvantages and adverse effects: • Helper Dependent Adenoviral vectors are invariably contaminated with miniscule Adeno helper virus which can illicit an immune response. • Immune responses against the transgene can still illicit an immune response. • Viral particles can be neutralized by the host immune response. • Short-term expression of the transgene due to lack of integration into the host genome. Cloning Helper Dependent Adenovirus Plasmids: The helper dependent adenovirus system uses two cloning steps to generate the helper dependent adenoviral genome: 1. The Shuttle Plasmid: The shuttle plasmid is usually cloned by the investigator and contains the gene of interest driven by the desired promoter and any other elements needed for a single or bicistronic construct. The MCS of the shuttle plasmid is inserted into a LacZ ORF. This allows for simple white-blue screening using X-gal. The gene cassette must not contain a PmeI site and must be free of BsiWI sites. BsiWI is used to cut out the gene cassette in the shuttle prior to cloning into the viral backbone AscI site by Gibson Assembly. The shuttle vector contains two small sections of stuffer sequences that help facilitate Gibson cloning. Once cloning is complete, PmeI is used to linearize the viral backbone prior to the initial transfection. The VVC also offers limited cloning services for investigators. The gene cassette will be cloned into the appropriate backbone plasmid once the shuttle plasmid is received by the VVC. 2. The Viral Backbone Plasmid: This plasmid contains the adenoviral packaging signal, an untranslated portion of the E4 gene, and stuffer sequences. The investigator’s gene cassette is moved from the pHDAdShuttle into the appropriate backbone by restriction digest and then Gibson assembly. Insert Size: Helper dependent Adenovirus vectors can accommodate inserts of up to 30kb, this includes promoters, gene(s) of interest, and other elements. Multiple viral backbones are available with varying sizes of stuffer sequences. Choosing which backbone to use depends on the size of the gene cassettes that will be inserted into them. E. coli Competent Cell Recommendations: We recommend using DH5alpha cells to grow the plasmids. Recommended Plasmid Quality Control: Sequencing: It is highly recommended to sequence all genes inserted into the viral shuttle plasmid before it is sent to us for virus construction. M13F and M13R primers flank the multiple cloning site. Protein Expression: The pUC57 based HDAdShuttle6 plasmid can act as an expression plasmid and it is therefore highly recommended that the shuttle plasmid be tested for protein expression prior to sending it to the VVC. Integrity Digest: We recommend that submitted plasmids be checked by diagnostic digest as well as sequencing. We suggest single restriction enzyme digestions with enzymes that cut the insert and backbone in multiple places. Helper Dependent Production Services: 1. Recombination, amplification, purification & titer • Shuttle: A cloning/expression adenovirus shuttle vector (see list below) is provided free of charge (not including shipping fees) after a Material Transfer Agreement is signed. • Sample required: 40ug of helper dependent adenovirus shuttle plasmid expressing the gene of interest at a concentration greater than 0.25ug/ul. Please note that DNA quality greatly affects virus production. • Time line: 5-8 weeks from the time the plasmid is received. • Service: o Cloning of shuttle insert into viral backbone. o Transfection and recombination. o Large-scale amplification. o Purification by: - Double cesium chloride gradient - With every new lot an infectious titer (IGU/ml) is provided. o Each lot is checked quantitatively for Adeno helper virus contamination . • Material provided: 2ml and a 100ul tester at a concentration of 1E+10 to 5E+10 IGU/ml (Infectious Genome Units/ml) • Vehicle: Helper Dependent Adenovirus vectors are resuspended in A195 buffer (See reference below) • Stock: The vector is kept in stock. Additional 1ml aliquots can be purchased but they can take several weeks to make. References: Helper Dependent Adenovirus: Palmer JD, and Ng P. Rescue, Amplification, and Large-Scale Production of Helper-Dependent Adenovirual Vectors: Cold Spring Harb Protoc; 2011; doi:10.1101/pdb.prot5627 Palmer JD and Ng P. Characterization of Helper-Dependent Adenoviral Vectors: Cold Spring Harb Protoc; 2011; doi: 10.1101/pdb.prot5628 Gallaher SD, Berk AJ. A rapid Q-PCR titration protocol for adenovirus and helper- dependent adenovirus vectors that produces biologically relevant results. Journal of Virological Methods 192 (2013) 28-38. RapAdTM System: Anderson RD, Haskell RE, Xia H, Roessler BJ, Davidson BL. “A simple method for the rapid generation of recombinant adenovirus vectors”. Gene Ther. 2000 Jun;7(12):1034-8 A195 Buffer: Evans RK, Nawrocki DK, Isopi LA, Williams DM, Casimiro DR, Chin S, Chen M, Zhu DM, Shiver JW, Volkin DB. Development of stable liquid formulations for adenovirus-based vaccines. J Pharm Sci. 2004 Oct;93(10):2458-7 Contact Information: Viral Vector Core University of Iowa 500 Newton Road 221 Eckstein Medical Research Building Iowa City, IA 52242 Tel: (319) 335-6726 [email protected] *version 9/18/15 SJS .
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