Plasmid DNA vaccine vector design: Impact on efficacy, safety and upstream production

Biotechnology Advances

Volumn 27, Issue 4, 2009, Pages 353-370

  Williams, James A ^a   Carnes, Aaron E ^a   Hodgson, Clague P ^a  

^a NATURE TECHNOLOGY CORPORATION   (United States)

Author keywords

DNA vaccine; Escherichia coli; Fermentation; Gene therapy; Plasmid; Vector

Indexed keywords

BACTERIAL PRODUCTIONS; BIOLOGICAL FACTORS; CLINICAL USE; DNA VACCINE; DRY CELLS; FOOD AND DRUG ADMINISTRATIONS; GENE THERAPY; HIGH YIELDS; MAMMALIAN CELLS; PLASMID; PLASMID DNAS; PRE-CLINICAL TESTING; REGULATORY GUIDANCES; SYNTHETIC GENES; VECTOR DESIGNS; WORLD HEALTH ORGANIZATIONS;

BIOCHEMICAL ENGINEERING; BIOINFORMATICS; DESIGN; DNA; ESCHERICHIA COLI; FERMENTATION; GENES; GENETIC ENGINEERING; MAMMALS; METABOLISM; NUCLEIC ACIDS; SAFETY ENGINEERING; SAFETY TESTING; VACCINES;

VECTORS;

DNA VACCINE;

BACTERIUM; BIOINFORMATICS; DNA; FERMENTATION; GENE EXPRESSION; MAMMAL; OPTIMIZATION; PLASMID; SAFETY; VACCINE; WORLD HEALTH ORGANIZATION;

ANIMAL; ESCHERICHIA COLI; FERMENTATION; GENE EXPRESSION; GENE THERAPY; GENE VECTOR; GENETICS; HUMAN; IMMUNOLOGY; MAMMAL; METABOLISM; METHODOLOGY; PLASMID; REVIEW; STANDARD;

ANIMALS; ESCHERICHIA COLI; FERMENTATION; GENE EXPRESSION; GENE THERAPY; GENETIC VECTORS; HUMANS; MAMMALS; PLASMIDS; VACCINES, DNA;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; MAMMALIA;

EID: 67349156033     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2009.02.003     Document Type: Review

References (184)

1. Abeel T., Saeys Y., Bonnet E., Rouze P., and Van de Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res 18 (2008) 310-323
2. Akerlund T., Nordstrom K., and Bernander R. Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli. J Bacteriol 177 (1995) 6791-6797
3. Allamane S., Jourdes P., Ratel D., Vicat J.M., Dupre I., Laine M., et al. Bacterial DNA methylation and gene transfer efficiency. Biochem Biophys Res Commun 276 (2000) 1261-1264
4. August JT, Pardoll DM, Guarnieri FG. Lysosomal targeting of immunogens. US Patent No. 5633234, 1997
5. Azzoni A.R., Ribeiro S.C., Monteiro G.A., and Prazeres D.M.F. The impact of polyadenylation signals on plasmid nuclease-resistance and transgene expression. J Gene Med 9 (2007) 392-402
6. Bakkali M. Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences. PLoS ONE 2 (2007) e741
7. Barouch D.H., Yang Z.Y., Kong W.P., Korioth-Schmitz B., Sumida S.M., Truitt D.M., et al. A human T-cell leukemia virus type 1 regulatory element enhances the immunogenicity of human immunodeficiency virus type 1 DNA vaccines in mice and nonhuman primates. J Virol 79 (2005) 8828-8834
8. Barros De Arruda L., Chickhlikar P.R., August J.T., and Marques E.T.A. DNA vaccine encoding human immunodeficiency virus-1 Gag, targeted to the major histocompatibility complex II compartment by lysosomal-associated membrane protein, elicits long-term memory response. Immunology 112 (2004) 126-133
9. Berg C.M., Liu L., Coon M., Stausbaugh L.D., Gray P., Vartak N.B., et al. pBR322-derived multicopy plasmids harboring large inserts are often dimers in Escherichia coli K-12. Plasmid 21 (1989) 138-141
10. Bernander R., Merryweather A., and Nordstrom K. Overinitiation of replication of the Escherichia coli chromosome from an integrated runaway-replication derivative of Plasmid R1. J Bacteriol 171 (1989) 674-683
11. Bi C.P., and Benham C.J. WebSIDD: server for prediction of the stress-induced duplex destabilized sites in superhelical DNA. Bioinformatics 20 (2004) 1477-1479
12. Bichara M., Schumacher S., and Fuchs R.P. Genetic instability within monotonous runs of CpG sequences in Escherichia coli. Genetics 140 (1995) 897-907
13. Bloquel C., Fabre E., Bureau M.F., and Scherman D. Plasmid DNA electrotransfer for intracellular and secreted proteins expression: new methodological developments and applications. J Gene Med Suppl 1 (2004) S11-S23
14. Boyd A.C., Popp F., Michaelis U., Davidson H., Davidson-Smith H., Doherty A., et al. Insertion of natural intron 6a-6b into a human cDNA-derived gene therapy vector for cystic fibrosis improves plasmid stability and permits facile RNA/DNA discrimination. J Gene Med 1 (1999) 312-321
15. Bremer H., and Dennis P.P. Modulation of chemical composition and other parameters of the cell by growth rate. In: Neidhardt F.C., Curtiss R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds). Escherichia coli and Salmonella. Cellular and molecular biology vol. 2 (1996), ASM Press, Washington 1553-1569
16. Brosius J. Toxicity of an overproduced foreign gene product in Escherichia coli and its use in plasmid vectors for the selection of transcription terminators. Gene 27 (1984) 161-172
17. Carnes A.E. Fermentation design for the manufacture of therapeutic plasmid DNA. BioProcess Int 3 (2005) 36-44
18. Carnes, A.E., Williams, J.A. Process for plasmid DNA fermentation. World Patent Application WO2006023546, 2006
19. Carnes A.E., and Williams J.A. Plasmid DNA manufacturing technology. Recent Pat Biotechnol 1 (2007) 151-156
20. Carnes A.E., Hodgson C.P., and Williams J.A. Inducible Escherichia coli fermentation for increased plasmid DNA production. Biotechnol Appl Biochem 45 (2006) 155-166
21. Carnes AE, Hodgson CP, Williams JA. Improved E. coli plasmid DNA production. World Patent Application WO 2009025690 2009.
22. Chalker A.F., Leach D.R., and Lloyd R.G. Escherichia coli sbcC mutants permit stable propagation of DNA replicons containing a long palindrome. Gene 71 (1988) 201-205
23. Chapman B.S., Thayer R.M., Vincent K.A., and Haigwood N.L. Effect of intron A from human cytomegalovirus (Towne) immediate-early gene on heterologous expression in mammalian cells. Nucleic Acids Res 19 (1991) 2979-2986
24. Cheah U.E., Weigand W.A., and Stark B.C. Effects of recombinant plasmid size on cellular processes in Escherichia coli. Plasmid 18 (1987) 127-134
25. Chen J.D., and Morrision D.A. Cloning of Streptococcus pneumoniae DNA fragments in Escherichia coli requires vectors protected by strong transcriptional terminators. Gene 55 (1987) 179-187
26. Chen W., Kallio P.T., and Bailey J.E. Construction and characterization of a novel cross-regulation system for regulating cloned gene expression in Escherichia coli. Gene 130 (1993) 15-22
27. Chen Z.Y., Riu E., He C.Y., Xu H., and Kay M.A. Silencing of episomal transgene expression in liver by plasmid bacterial backbone DNA is independent of CpG methylation. Molec Ther 16 (2008) 548-556
28. Chiang C.S., and Bremer H. Stability of pBR322-derived plasmids. Plasmid 20 (1988) 207-220
29. Churchward G., Bremer H., and Young R. Macromolecular composition of bacteria. J Theor Biol 94 (1982) 651-670
30. Connelly J.C., and Leach D.R. The sbcC and sbcD genes of Escherichia coli encode a nuclease involved in palindrome inviability and genetic recombination. Genes Cells 1 (1996) 285-291
31. Connelly J.C., de Leau E.S., and Leach D.R. DNA cleavage and degradation by the SbcCD protein complex from Escherichia coli. Nucleic Acids Res 27 (1999) 1039-1046
32. Cooke J.R., McKie E.A., Ward J.M., and Keshavarz-Moore E. Impact of intrinsic DNA structure on processing of plasmids for gene therapy and DNA vaccines. J Biotechnol 114 (2004) 239-254
33. Cranenburgh, R.M. Plasmid Maintenance. World Patent Application WO2005052167, 2005
34. Cranenburgh R.M., Hanak J.A., Williams S.G., and Sherratt D.J. Escherichia coli strains that allow antibiotic-free plasmid selection and maintenance by repressor titration. Nucleic Acids Res 29 (2001) E26
35. Cromie G.A., Millar C.B., Schmidt K.H., and Leach D.R. Palindromes as substrates for multiple pathways of recombination in Escherichia coli. Genetics 154 (2000) 513-522
36. Crouzet J, Cameron B. Method for producing therapeutic DNA. US Patent Application No 20020187527, 2002
37. Danquah M.K., and Forde G.M. Development of a pilot-scale bacterial fermentation for plasmid based biopharmaceutical production using stoichiometric medium. Biotechnol Bioprocess Eng 13 (2008) 158-167
38. Darquet A.M., Cameron B., Wils P., Scherman D., and Crouzet J. A new DNA vehicle for nonviral gene delivery: supercoiled minicircles. Gene Ther 4 (1997) 1341-1349
39. Delogu G., Howard A., Collins F.M., and Morris S.L. DNA vaccination against tuberculosis: expression of a ubiquitin-conjugated tuberculosis protein enhances antimycobacterial immunity. Infect Immun 68 (2000) 3097-3102
40. Del Solar G., Giraldo R., Ruiz-Echevarria M.J., Espinosa M., and Diaz-Orejas R. Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62 (1998) 434-464
41. Durland R.H., and Eastman E.M. Manufacturing and quality control of plasmid-based gene expression systems. Adv Drug Deliv Rev 30 (1998) 33-48
42. EMEA. Note for guidance on the quality, preclinical and clinical aspects of gene transfer medicinal products. European Medicines Agency Doc. Ref. CPMP/BWP/3088/99 (2001)
43. EMEA. Guideline on non-clinical studies required before first clinical use of gene therapy medicinal product. European Medicines Agency Doc. Ref. EMEA/CHMP/GTWP/125459/2006 (2006)
44. EMEA. Overview of comments received on guideline on non-clinical studies required before first clinical use of gene therapy medicinal products. European Medicines Agency Doc. Ref. EMEA/CHMP/GTWP/65260/2008 (2008)
45. Engels P., and Meyer P. Inactivation of the transcriptional-dependent inhibition of plasmid replication: a selection method for cloning large DNA fragments. BioTechniques 14 (1993) 324-325
46. FDA. Points to consider on plasmid DNA vaccines for preventive infectious disease indications (1996), US Food and Drug Administration
47. FDA. Guidance for industry: guidance for human somatic cell therapy and gene therapy (1998), US Food and Drug Administration
48. FDA. Guidance for industry: considerations for plasmid DNA vaccines for infectious disease indications (2007), US Food and Drug Administration
49. Fishel R.A., James A.A., and Kolodner R. recA-independent general genetic recombination of plasmids. Nature 294 (1981) 184-186
50. Flores S., Anda-Herrera R., Gosset G., and Bolivar F.G. Growth-rate recovery of Escherichia coli cultures carrying a multicopy plasmid, by engineering of the pentose-phosphate pathway. Biotechnol Bioeng 87 (2004) 485-494
51. Fuller, J. Nucleic Acid Constructs. World Patent Application WO2006082398, 2006
52. Gerber L., Kodukula K., and Udenfriend S. Phosphatidylinositol glycan (PI-G) anchored membrane proteins. J Biol Chem 267 (1992) 12168-12173
53. Ghersa P., Whelan J., Pescini R., DeLamarter J.F., and Hooft van Huijsduijnen R. Commonly used cat reporter vectors contain a cAMP-inducible, cryptic enhancer that co-operates with NF-kappa B-sites. Gene 151 (1994) 331-332
54. Glenting J., and Wessels S. Ensuring safety of DNA vaccines. Microb Cell Fact 4 (2005) 26-31
55. Glick B.R. Metabolic load and heterologous gene expression. Biotechnol Adv 13 (1995) 247-261
56. Glickman B.W., and Radman M. Escherichia coli mutator mutants deficient in methylation-instructed DNA mismatch correction. Proc Natl Acad Sci U S A 77 (1980) 1063-1067
57. Gomez-Eichelmann M.C., Levy-Mustri A., and Ramirez-Santos J. Presence of 5-methylcytosine in CC(A/T)GG sequences (dcm methylation) in DNAs from different bacteria. J Bacteriol 173 (1991) 7692-7694
58. Grabherr, R., Pfaffenzeller, I. Host-vector system for antibiotic-free ColE1 plasmid propagation. World Patent Application WO2006029985, 2006.
59. Gu W., Zhou T., Ma J., Sun X., and Lu Z. Folding type specific secondary structure propensities of synonymous codons. IEEE Trans Nanobioscience 2 (2003) 150-157
60. Gursel I., Gursel M., Yamada H., Ishii K.J., Takeshita F., and Klinman D.M. Repetitive elements in mammalian telomeres suppress bacterial DNA-induced immune activation. J Immunol 171 (2003) 1393-1400
61. Hamann CW, Nielsen J, Ingersle E. Novel plasmids for use in medicine and method of producing same. World Patent Application WO0028048, 2002
62. Hartikka J., Sawdey M., Cornefert-Jensen F., Margalith M., Barnhart K., et al. An improved plasmid DNA expression vector for direct injection into skeletal muscle. Hum Gene Ther 7 (1996) 1205-1217
63. Hebel H.L., Cai Y., Davies L.A., Hyde S.C., Pringle I.A., and Gill D.R. Challenges in the process development of a novel zero-CpG CFTR plasmid for human clinical use. ASGT (2008)
64. Ho P.S., Ellison M.J., Quigley G.J., and Rich A. A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J 5 (1986) 2737-2744
65. 3 fermentation scale for an influenza pandemic. Biotechnol Prog 21 (2005) 1577-1592
66. Hofmann K.H., Neubauer P., Riethdorf S., and Hecker M. Amplification of pBR322 plasmid DNA in Escherichia coli relA strains during batch and fed-batch fermentation. J Basic Microbiol 30 (1990) 37-41
67. Huang Y., Krasnitz M., Rabadan R., Witten D.M., Song Y., Levine A.J., et al. A recoding method to improve the humoral response to an HIV DNA vaccine. PLoS ONE 3 (2008) e3214
68. Huber H, Pacher C, Necina R, Kollmann F, Reinisch C. Method for producing plasmid DNA on a manufacturing scale by fermentation of the Escherichia coli K-12 strain JM108. World Patent Application WO2005098002, 2005a
69. Huber H, Weigl G, Buchinger W. Fed-batch fermentation process and culture medium for the production of plasmid DNA in E. coli on a manufacturing scale. World Patent Application WO2005097990, 2005b
70. Ioshiknhes I., Roy S., and Sen C.K. Algorithms for mapping of mRNA targets for MicroRNA. DNA Cell Biol 26 (2007) 265-272
71. Ishii K.J., Kawagoe T., Koyama S., Matsui K., Kumar H., Kawai T., et al. TANK-binding kinase-1 delineates innate and adaptive immune responses to DNA vaccines. Nature 451 (2008) 725-729
72. Kato M. Polypyrimidine/polypurine sequence in plasmid DNA enhances formation of dimer molecules in Escherichia coli. Dimerization of plasmid DNA in Escherichia coli. Mol Biol Rep 18 (1993) 183-187
73. Kay A., O'Kennedy R.D., Ward J., and Keshavarz-Moore E. Impact of plasmid size on cellular oxygen demand in Escherichia coli. Biotechnol Appl Biochem 38 (2003) 1-7
74. Kong S., Rock C.F., Booth A., Willoughby N., O'Kennedy R.D., Relton J., et al. Large-scale plasmid DNA processing: evidence that cell harvesting and storage methods affect yield of supercoiled plasmid DNA. Biotechnol Appl Biochem 51 (2008) 43-51
75. Kozak M. Recognition of AUG and alternative initiator codons is augmented by G in position + 4 but is not generally affected by the nucleotides in position + 5 and + 6. EMBO J 16 (1997) 2482-2492
76. Krieg A.M. Direct immunologic activities of CpG DNA and implications for gene therapy. J Gene Med 1 (1999) 56-63
77. Krieg A.M, Davis HL, Wu T, Schorr J. Vectors and methods for immunization or therapeutic protocols. United States Patent 6339068, 2002
78. Kushner P.J., Baxter J.D., Duncan K.G., Lopez G.N., Schaufele F., Uht R.M., et al. Eukaryotic regulatory elements lurking in plasmid DNA: the activator protein-1 site in pUC. Mol Endocrinol 8 (1994) 405-407
79. Kutzler M.A., and Weiner D.B. DNA vaccines: ready for prime time?. Nat Rev Genet 9 (2008) 776-788
80. Laddy D.J., Yan J., Corbitt N., Kobasa D., Kobinger G.P., and Weiner D.B. Immunogenicity of novel consensus-based DNA vaccines against avian influenza. Vaccine 25 (2007) 2984-2989
81. Lahijani R., Hulley G., Soriano G., Horn N.A., and Marquet M. High-yield production of pBR322-derived plasmids intended for human gene therapy by employing a temperature-controllable point mutation. Hum Gene Ther 7 (1996) 1971-1980
82. Lai Y.F., Tseng Y.J., Yang F.Y., and Au L.C. Mammalian cis-reporting plasmid may alter activities due to the derivation of host Escherichia coli strains. Anal Biochem 376 (2008) 103-107
83. Lee J., Him H.C., Kim S.W., Hong S.I., and Park Y.H. Interplay of SOS induction, recombinant gene expression, and multimerization of plasmid vectors in Escherichia coli. Biotechnol Bioeng 80 (2002) 84-92
84. Leifert J.A., Rodriguez-Carreno M.P., Rodriguez F., and Whitton J.L. Targeting plasmid-encoded proteins to the antigen presentation pathways. Immunol Rev 199 (2004) 40-53
85. Leite J.P., Cousin C., Heysen A., and D'Halluin J.C. Negative effect of a cis-acting pBR322 element on adenovirus E1a gene expression. Gene 82 (1989) 351-356
86. Levy, J. Avoidance of undesirable replication intermediates in plasmid propagation. US Patent 7390654, 2003
87. Li S., MacLaughlin F.C., Fewell J.G., Gondo M., Wang J., Nicol F., et al. Muscle-specific enhancement of gene expression by incorporation of SV40 enhancer in the expression plasmid. Gene Ther 8 (2001) 494-497
88. Li H.S., Liu Y., Li D.F., Zhang R.R., Tang H.L., Zhang Y.W., et al. Enhancement of DNA vaccine-induced immune responses by a 72-bp element from SV40 enhancer. Chin Med J 120 (2007) 496-502
89. Lin-Chao S., and Bremer H. Effect of the bacterial growth rate on replication control of plasmid pBR322 in Escherichia coli. Mol Gen Genet 203 (1986) 143-149
90. Lin-Chao S., Chen W., and Wong T. High copy number of the pUC plasmid results from a Rom/Rop-suppressible point mutation in RNAII. Mol Microbiol 6 (1992) 3385-3393
91. Listner K., Bentley L., Okonkowski J., Kistler C., Wnek R., Caparoni A., et al. Development of a highly productive and scalable plasmid DNA production platform. Biotechnol Prog 22 (2006) 1335-1345
92. Lobner-Olesen A., Skovgaard O., and Marinus M.G. Dam methylation: coordinating cellular processes. Curr Opin Microbiol 8 (2005) 154-160
93. Luke J, Carnes A.E, Hodgson C.P, Williams JA. Improved antibiotic-free DNA vaccine vectors utilizing a novel RNA based plasmid selection system. Vaccine, in press
94. Mairhofer J., and Grabherr R. Rational vector design for efficient non-viral gene delivery: challenges facing the use of plasmid DNA. Mol Biotechnol 39 (2008) 97-104
95. Mairhofer J., Pfaffenzeller I., Merz D., and Grabherr R. A novel antibiotic free plasmid selection system: advances in safe and efficient DNA therapy. Biotechnol J 3 (2008) 83-89
96. Manoj S., Babiuk L.A., and van Drunen Littel-van den Hurk S. Approaches to enhance the efficacy of DNA vaccines. Crit Rev Clin Lab Sci 41 (2004) 1-39
97. Marinus M.G., Carraway M., Frey A.Z., Brown L., and Arraj A.J. Insertion mutants in the dam gene of Escherichia coli K-12. Mol Gen Genet 192 (1983) 288-289
98. Masai H., and Arai K. Mechanisms of primer RNA synthesis and D-loop/R-loop-dependent DNA replication in Escherichia coli. Biochimie 78 (1996) 1109-1117
99. McGlynn P., and Guy C.P. Replication forks blocked by protein-DNA complexes have limited stability in vitro. J Mol Biol 381 (2008) 249-255
100. Middaugh C.R., Evans R.K., Montgomery D.L., and Casimiro D.R. Analysis of plasmid DNA from a pharmaceutical perspective. J Pharm Sci 87 (1997) 130-146
101. Mirkin E.V., and Mirkin S.M. Replication fork stalling at natural impediments. Microbiol Mol Biol Rev 71 (2007) 13-35
102. Neylon C., Kralicek A.V., Hill T.M., and Dixon N.E. Replication termination in E. coli: structure and antihelicase activity of the Tus-Ter complex. Microbiol Mol Biol Rev 69 (2005) 501-526
103. Nordstrom K., and Uhlin B.E. Runway replication plasmids as tools to produce large quantities of proteins from cloned genes in bacteria. Bio/Technology 10 (1992) 661-666
104. Ochiai H., Harashima H., and Kamiya H. Effect of methylated adenine in plasmid DNA on transgene expression in mice. Biol Pharm Bull 28 (2005) 2019-2022
105. O'Kennedy R.D., Baldwin C., and Keshavarz-Moore E. Effects of growth medium selection on plasmid DNA production and initial processing steps. J Biotechnol 76 (2000) 175-183
106. O'Kennedy R.D., Ward J.M., and Keshavarz-Moore E. Effects of fermentation strategy on the characteristics of plasmid DNA production. Biotechnol Appl Biochem 37 (2003) 83-90
107. O'Mahony K., Freitag R., Hilbrig F., Muller P., and Schumacher I. Strategies for high titre plasmid DNA production in Escherichia coli DH5α. Process Biochem 42 (2007) 1039-1049
108. Ow D.S., Lee R.M., Nissom P.M., Philp R., Oh S.K., and Yap M.G. Inactivating FruR global regulator in plasmid-bearing Escherichia coli alters metabolic gene expression and improves growth rate. J Biotechnol 131 (2007) 261-269
109. Ow D.S., Yap M.G., and Oh S.K. Enhancement of plasmid DNA yields during fed-batch culture with a fruR knockout Escherichia coli strain. Biotechnol Appl Biochem 52 (2009) 53-59
110. Pan X., and Leach D.R. The roles of mutS, sbcCD and recA in the propagation of TGG repeats in Escherichia coli. Nucleic Acids Res 28 (2000) 3178-3184
111. Pertea M., Lin X., and Salzberg S.L. GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res 29 (2001) 1185-1190
112. Peterson D.O., Beifuss K.K., and Morley K.L. Context-dependent gene expression: cis-acting negative effects of specific prokaryotic plasmid sequences on eukaryotic genes. Mol Cell Biol 7 (1987) 1563-1567
113. Phue J.N., Lee S.J., Trinh L., and Shiloach J. Modified Escherichia coli B (BL21), a superior producer of plasmid DNA compared with Escherichia coli K (DH5α). Biotechnol Bioeng 101 (2008) 831-836
114. Posfai G., Plunkett III G., Feher T., Frisch D., Keil G.M., Umenhoffer K., et al. Emergent properties of reduced-genome Escherichia coli. Science 312 (2006) 1044-1046
115. Prather K.J., Sagar S., Murphy J., and Chartrain M. Industrial scale production of plasmid DNA for vaccine and gene therapy: plasmid design, production and purification. Enzyme Microb Technol 33 (2003) 865-883
116. Prather K.L., Edmonds M.C., and Herod J.W. Identification and characterization of IS1 transposition in plasmid amplification mutants of E. coli clones producing DNA vaccines. Appl Microbiol Biotechnol 73 (2006) 815-826
117. Puigbo P., Guzman E., Romeu A., and Garcia-Vallve S. Optimizer: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res 35 (2007) W126-W131
118. Qiu J.T., Liu B., Tian C., Pavlakis G., and Yu X.F. Enhancement of primary and secondary cellular immune responses against human immunodeficiency virus type 1 gag by using DNA expression vectors that target gag antigen to the secretory pathway. J Virol 74 (2000) 5997-6005
119. Ramanathan M.P., Ayyavoo V., and Weiner D.B. Choice of expression vector alters the localization of a human cellular protein. DNA Cell Biol 20 (2001) 101-105
120. Ribeiro S.C., Monteiro G.A., and Prazeres D.M.F. Evaluation of the effect of non-B DNA structures on plasmid integrity via accelerated stability studies. J Pharm Sci (2008) (Epub)
121. Ribeiro S.C., Oliveira P.H., Prazeres D.M., and Monteiro G.A. High frequency plasmid recombination mediated by 28 bp direct repeats. Mol Biotechnol 40 (2008) 252-260
122. Ricci J.C.D., and Hernandez M.E. Plasmid effects on Escherichia coli metabolism. Crit Rev Biotechnol 20 (2000) 79-108
123. Rice P., Longden I., and Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 16 (2000) 276-277
124. Roberts T.L., Dunn J.A., Terry T.D., Jennings M.P., Hume D.A., Sweet M.J., et al. Differences in macrophage activation by bacterial DNA and CpG-containing oligonucleotides. J Immunol 175 (2005) 3569-3576
125. Rodriguez F., An L.L., Harkins S., Zhang J., Yokoyama M., Widera G., et al. DNA immunization with minigenes: low frequency of memory cytotoxic T lymphocytes and inefficient antiviral protection are rectified by ubiquitination. J Virol 72 (1998) 5174-5181
126. Rozkov A., Avignone-Rossa C.A., Ertl P.F., Jones P., O'Kennedy R.D., Smith J.J., et al. Characterization of the metabolic burden on Escherichia coli DH1 cells imposed by the presence of a plasmid containing a gene therapy sequence. Biotechnol Bioeng 88 (2004) 909-915
127. Saida F., Uzan M., Odaert B., and Bontems F. Expression of highly toxic genes in E. coli: special strategies and genetic tools. Curr Protein Pept Sci 7 (2006) 47-56
128. Schalk J.A., Mooi F.R., Berbers G.A., van Aerts L.A., Ovelgonne H., and Kimman T.G. Preclinical and clinical safety studies on DNA vaccines. Hum Vaccines 2 (2006) 45-53
129. Schirmbeck R., Riedl P., Fissolo N., Lemonnier F.A., Bertoleti A., and Reimann J. Translation from cryptic reading frames of DNA vaccines generates an extended repertoire of immunogenic, MHC Class I-restricted epitopes. J Immunol 174 (2005) 4647-4656
130. Schmidt T, Friehs K, Flaschel E, Schleef M. Method for the isolation of ccc plasmid DNA. US Patent 6664078, 2003
131. Schroeter A., Riethdorf S., and Hecker M. Amplification of different ColE1 plasmids in an Escherichia coli relA strain. J Basic Microbiol 28 (1988) 553-555
132. Seo J.H., and Bailey J.E. Effects of recombinant plasmid content on growth properties and cloned gene product formation in Escherichia coli. Biotechnol Bioeng 27 (1985) 1668-1674
133. Shamlou P.A. Scaleable processes for the manufacture of therapeutic quantities of plasmid DNA. Biotechnol Appl Biochem 37 (2003) 207-218
134. Sheets R.L., Stein J., Manetz T.S., Andrews C., Bailer R., Rathmann J., et al. Toxicological safety evaluation of DNA plasmid vaccines against HIV-1, Ebola, Severe Acute Respiratory Syndrome, or West Nile virus is similar despite differing plasmid backbones or gene-inserts. Toxicol Sci 91 (2006) 620--630
135. Sheets R.L., Stein J., Manetz T.S., Duffy C., Nason M., Andrews C., et al. Biodistribution of DNA plasmid vaccines against HIV-1, Ebola, Severe Acute Respiratory Syndrome, or West Nile virus is similar, without integration, despite differing plasmid backbones or gene insert. Toxicol Sci 91 (2006) 610-619
136. Sherratt DJ, Williams SG, Hanak JAJ. Plasmid stabilization. US Patent No 5972708, 1999
137. Shiloach J., and Fass R. Growing E. coli to high cell density - a historical perspective on method development. Biotechnol Adv 23 (2005) 345-357
138. Singer A., Eiteman M.A., and Altman E. DNA plasmid production in different host strains of Escherichia coli. J Ind Microbiol Biotech (2009) (epub)
139. Siregar J.J., Lerner S.A., and Mobashery S. Purification and characterization of aminoglycoside 3′-phosphotransferase Type IIa and kinetic comparison with a new mutant enzyme. Antimicrob Agents Chemother 38 (1994) 641-647
140. Siregar J.J., Miroshnikov K., and Mobashery S. Purification, characterization, and investigation of the mechanism of aminoglycoside 3′-phosphotransferase Type Ia. Biochemistry 34 (1995) 12641-12688
141. Skarstad K., Steen H.B., and Boye E. Escherichia coli DNA distributions measured by flow cytometry and compared with theoretical computer simulations. J Bacteriol 163 (1985) 661-668
142. Snyder LA, Satishchandran C. Chimeric kanamycin resistance gene. US Patent 5851804, 1998
143. Soubrier, F. Circular DNA molecule having a conditional origin of replication, process for their preparation and their use in gene therapy. World Patent Application WO2004033664, 2004
144. Soubrier F., Cameron B., Manse B., Somarriba S., Dubertret C., Jaslin G., et al. pCOR: a new design of plasmid vectors for nonviral gene therapy. Gene Ther 6 (1999) 1482-1488
145. Soubrier F., Laborderie B., and Cameron B. Improvement of pCOR plasmid copy number for pharmaceutical applications. Appl Microbiol Biotechnol 66 (2005) 683-688
146. Summers D. Timing, self-control and a sense of direction are the secrets of multicopy plasmid stability. Mol Microbiol 29 (1998) 1137-1145
147. Summers D.K., Beton C.W., and Withers H.L. Multicopy plasmid instability: the dimer catastrophe hypothesis. Mol Microbiol 8 (1993) 1031-1038
148. Szpirer C.Y., and Milinkovitch M.C. Separate-component-stabilization system for protein and DNA production without the use of antibiotics. BioTechniques 38 (2005) 775-781
149. Tachedjian M., Boyle J.S., Lew A.M., Horvatic B., Scheerlinck J.P., Tennent J.M., et al. Gene gun immunization in a preclinical model is enhanced by B7 targeting. Vaccine 21 (2003) 2900-2905
150. Takeshita F., and Ishii K.J. Intracellular DNA sensors in immunity. Curr Opin Immunol 20 (2008) 383-388
151. Trevani A.S., Chorny A., Salamone G., Vermeulen M., Gamberale R., Schettini J., et al. Bacterial DNA activates human neutrophils by a CpG-independent pathway. Eur J Immunol 33 (2003) 3164-3174
152. Tsuchiya H., Matsuda T., Harashima H., and Kamiya H. Cytokine induction by a bacterial DNA-specific modified base. Biochem Biophys Res Commun 326 (2005) 777-781
153. Tully D.B., and Cidlowski J.A. pBR322 contains glucocorticoid regulatory element DNA consensus sequences. Biochem Biophys Res Commun 144 (1987) 1-10
154. Uhlin B.E., and Nordstrom K. A runaway-replication mutant of plasmid R1drd-19: temperature-dependent loss of copy number control. Mol Gen Genet 165 (1978) 167-179
155. Uhlin B.E., Molin S., Gustafsson P., and Nordstrom K. Plasmids with temperature-dependent copy number for amplification of cloned genes and their products. Gene 6 (1979) 91-106
156. Valenzuela M.S., Ikpeazu E.V., and Siddiqui K.A. E. coli growth inhibition by a high copy number derivative of plasmid pBR322. Biochem Biophys Res Commun 219 (1996) 876--883
157. Valenzuela M.S., Siddiqui K.A., and Sarkar B.L. High expression of plasmid-encoded tetracycline resistance gene in E. coli causes a decrease in membrane-bound ATPase activity. Plasmid 36 (1996) 19-25
158. van Hall T., van de Rhee N.E., Schoenberger S.P., Vierboom M.P., Verreck F.A., Melief C.J., et al. Cryptic open reading frames in plasmid vector backbone sequences can provide highly immunogenic cytotoxic T-lymphocyte epitopes. Cancer Res 58 (1998) 3087-3093
159. Villalobos A., Ness J.E., Gustafsson C., Minshull J., and Govindarajan S. Gene designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 7 (2006) 285
160. Wagner H. The sweetness of the DNA backbone drives toll-like receptor 9. Curr Opin Immunol 20 (2008) 396-400
161. Wagner E.G., and Brantl S. Kissing and RNA stability in antisense control of plasmid replication. TIBS 23 (1998) 451-454
162. Wang H., and Benham C.J. Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. BMC Bioinformatics 7 (2006) 248
163. Wang Z., Troilo P.J., Wang X., Griffiths T.G., Pacchione S.J., Barnum A.B., et al. Detection of integration of plasmid DNA into host genomic DNA following intramuscular injection and electroporation. Gene Ther 11 (2004) 711-721
164. Wang Z., Yuan Z., and Hengge U.R. Processing of plasmid DNA with ColE1-like replication origin. Plasmid 51 (2004) 149-161
165. Wang Z., Xiang L., Shao J., Wegrzyn A., and Wegrzyn G. Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb Cell Fact 5 (2006) 34
166. Weiner DB, Zhang D, Cohen A. Expression system for cloning toxic genes. United States Patent 6881558, 2005
167. Weiss R., Durnberger J., Mostbock S., Scheiblhofer S., Hartl A., Breitenbach M., et al. Improvement of the immune response against plasmid DNA encoding OspC of Borrelia by an ER-targeting leader sequence. Vaccine 18 (2000) 815-824
168. WHO. Annex 1: Guidelines for assuring the quality and nonclinical safety evaluation of DNA vaccines. World Heath Organization Technical Report Series No 941 (2007)
169. Williams JA. Vectors and methods for genetic immunization. World Patent Application WO2006078979, 2006
170. Williams, J.A. Vectors and methods for genetic immunization. World Patent Application WO2008153733, 2008
171. Williams J.A., Luke J., Johnson L., and Hodgson C. pDNAVACCultra vector family: high throughput intracellular targeting DNA vaccine plasmids. Vaccine 24 (2006) 4671-4676
172. Williams JA, Luke J, Langtry S, Anderson S, Hodgson CP, Carnes AE. Generic plasmid DNA production platform incorporating low metabolic burden seed-stock and fed-batch fermentation processes. Biotechnol. Bioeng., submitted for publication. doi:10.1002/bit.22347
173. Wong E.M., Muesing M.A., and Polisky B. Temperature-sensitive copy number mutants of ColE1 are located in an untranslated region of the plasmid genome. Proc Natl Acad Sci U S A 79 (1982) 3570-3574
174. Wu T., Guarnieri F.G., Staveley-O'Carroll K.F., Viscidi R.P., Levitsky H.I., Hedrick L., et al. Engineering an intracellular pathway for major histocompatibility complex class II presentation of antigens. Proc Natl Acad Sci U S A 92 (1995) 11671-11675
175. Wu G., Dress L., and Freeland S.J. Optimal encoding rules for synthetic genes: the need for a community effort. Mol Syst Biol 3 (2007) 134
176. Xu W., Chu Y., Zhang R., Xu H., Wang Y., and Xiong S. Endoplasmic reticulum targeting sequence enhances HBV-specific cytotoxic T lyphocytes induced by a CTL epitope-based DNA vaccine. Virology 334 (2005) 255-263
177. Yau S.Y., Keshavarz-Moore E., and Ward J. Host strain influences on supercoiled plasmid DNA production in Escherichia coli: implications for efficient design of large-scale processes. Biotechnol Bioeng 101 (2008) 529-544
178. Yew N.S., Zhao H., Przybylska M., Wu I.H., Tousignant J.D., Scheule R.K., et al. CpG-depleted plasmid DNA vectors with enhanced safety and long-term gene expression in vivo. Molec Ther 5 (2002) 731-738
179. Yuh C.H., and Ting L.P. The genome of hepatitis B virus contains a second enhancer: cooperation of two elements within this enhancer is required for its function. J Virol 64 (1990) 4281-4287
180. Zaman M.M., and Boles T.C. Plasmid recombination by the RecBCD pathway of Escherichia coli. J Bacteriol 178 (1996) 3840-3845
181. Zhongming L., Howard A., Kelley C., Delogu G., Collins F., and Morris S. Immunogenicity of DNA vaccines expressing tuberculosis proteins fused to tissue plasminogen activator signal sequences. Infect Immun 67 (1999) 4780-4786
182. Zielenkiewicz U., and Ceglowsik P. Mechanism of plasmid stable maintenance with special focus on plasmid addiction systems. Acta Biochim Pol 48 (2001) 1003-1023
183. Zinckgraf J.W., and Silbart L.K. Modulating gene expression using DNA vaccines with different 3′-UTRs influence antibody titer, seroconversion and cytokine profiles. Vaccine 21 (2002) 1640-1649
184. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31 (2003) 3406-3415