Quantification of cytosolic plasmid DNA degradation using high‐throughput sequencing: implications for gene delivery
dc.contributor.author | Rattan, Rahul | en_US |
dc.contributor.author | Bielinska, Anna U. | en_US |
dc.contributor.author | Banaszak Holl, Mark M. | en_US |
dc.date.accessioned | 2014-05-23T15:59:45Z | |
dc.date.available | 2015-05-04T14:37:25Z | en_US |
dc.date.issued | 2014-03 | en_US |
dc.identifier.citation | Rattan, Rahul; Bielinska, Anna U.; Banaszak Holl, Mark M. (2014). "Quantification of cytosolic plasmid DNA degradation using high‐throughput sequencing: implications for gene delivery." The Journal of Gene Medicine 16(3-4): 75-83. | en_US |
dc.identifier.issn | 1099-498X | en_US |
dc.identifier.issn | 1521-2254 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/106947 | |
dc.description.abstract | Background Although cytosolic DNA degradation plays an important role in decreasing transgene expression, the plasmid degradation pattern remains largely unexplored. Methods Illumina dye sequencing was employed to provide degradation site information for S1 and cytosolic nucleases. S1 nuclease provided a positive control for a comparison between the agarose gel method and sequencing approaches. Results The poly(A) region between the β‐lactamase gene and the cytomegalovirus (CMV) promoter was identified as the most likely cut site for polyplex‐treated cytosol. The second most likely site, at the 5' end of the β‐lactamase gene, was identified by gel electrophoresis and sequencing. Additional sites were detected in the OriC region, the SV40/poly(A) region, the luciferase gene and the CMV promoter. Sequence analysis of plasmid treated with cytosol from control cells showed the greatest cut activity in the OriC region, the β‐lactamase gene and the poly(A) region following the luciferase gene. Additional regions of cut activity include the SV40 promoter and the β‐lactamase poly(A) termination sequence. Both cytosolic nucleases and the S1 nuclease showed substantial activity at the bacterial origin of replication ( OriC ). Conclusions High‐throughput plasmid sequencing revealed regions of the luciferase plasmid DNA sequence that are sensitive to cytosolic nuclease degradation. This provides new targets for improving plasmid and/or polymer design to optimize the likelihood of protein expression. Copyright © 2014 John Wiley & Sons, Ltd. | en_US |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | HeLa | en_US |
dc.subject.other | Biotechnology | en_US |
dc.subject.other | Plasmid Design | en_US |
dc.subject.other | Plasmid Gene Delivery | en_US |
dc.subject.other | Polymer Vector | en_US |
dc.title | Quantification of cytosolic plasmid DNA degradation using high‐throughput sequencing: implications for gene delivery | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Genetics | en_US |
dc.subject.hlbsecondlevel | Molecular, Cellular and Developmental Biology | en_US |
dc.subject.hlbsecondlevel | Biological Chemistry | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/106947/1/jgm2761.pdf | |
dc.identifier.doi | 10.1002/jgm.2761 | en_US |
dc.identifier.source | The Journal of Gene Medicine | en_US |
dc.identifier.citedreference | Rattan R, Vaidyanathan S, Wu G, et al. Polyplex‐induced cytosolic nuclease activation leads to differential transgene expression. Mol Pharm 2013; 10: 3013 – 3022. | en_US |
dc.identifier.citedreference | Ribeiro SC, Monteiro GA, Prazeres DMF. The role of polyadenylation signal secondary structures on the resistance of plasmid vectors to nucleases. J Gene Med 2004; 6: 565 – 573. | en_US |
dc.identifier.citedreference | Condreay JP, Witherspoon SM, Clay WC, et al. Transient and stable gene expression in mammalian cells transduced with a recombinant baculovirus vector. Proc Natl Acad Sci U S A 1999; 96: 127 – 132. | en_US |
dc.identifier.citedreference | Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010; 2010: pdb.prot5448. | en_US |
dc.identifier.citedreference | Hoffman EK, Trusko SP, Murphy M, et al. An S1 nuclease‐sensitive homopurine/homopyrimidine domain in the c‐Ki‐ras promoter interacts with a nuclease factor. Proc Natl Acad Sci U S A 1990; 87: 2705 – 2709. | en_US |
dc.identifier.citedreference | Varkouhi AK, Scholte M, Storm G, et al. Endosomal escape pathways for delivery of biologicals. J Control Release 2011; 151: 220 – 228. | en_US |
dc.identifier.citedreference | Cho YW, Kim J‐D, Park K. Polycation gene delivery systems: escape from endosomes to cytosol. J Pharm Pharmacol 2003; 55: 721 – 734. | en_US |
dc.identifier.citedreference | Lechardeur D, Verkman AS, Lukacs GL. Intracellular routing of plasmid DNA during non‐viral gene transfer. Adv Drug Deliv Rev 2005; 57: 755 – 767. | en_US |
dc.identifier.citedreference | Dean D, Strong D, Zimmer W. Nuclear entry of nonviral vectors. Gene Ther 2005; 12: 881 – 890. | en_US |
dc.identifier.citedreference | Lechardeur D, Sohn KJ, Haardt M, et al. Metabolic instability of plasmid DNA in the cytosol: a potential barrier to gene transfer. Gene Ther 1999; 4: 482 – 497. | en_US |
dc.identifier.citedreference | Pollard H, Toumaniantz G, Amos J‐L, et al. Ca 2+ ‐sensitive cytosolic nucleases prevent efficient delivery to the nucleus of injected plasmids. J Gene Med 2001; 3: 153 – 164. | en_US |
dc.identifier.citedreference | Azzoni AR, Ribeiro SC, Monteiro GA, et al. The impact of polyadenylation signals on plasmid nuclease‐resistance and transgene expression. J Gene Med 2007; 9: 392 – 402. | en_US |
dc.identifier.citedreference | Nasheuer H‐P, Smith R, Bauerschmidt C, et al. Initiation of eukaryotic DNA replication: regulation and mechanisms. Prog Nucleic Acid Res Mol Biol 2002; 72: 41 – 93. | en_US |
dc.identifier.citedreference | Mott ML, Berger JM. DNA replication initiation: mechanisms and regulation in bacteria. Nature Rev Microbiol 2007; 5: 343 – 354. | en_US |
dc.identifier.citedreference | Rao BS. Regulation of DNA replication by homopurine/homopyrimidine sequences. Mol Cell Biochem 1996; 2: 163 – 168. | en_US |
dc.identifier.citedreference | Solymosy F, Fedorcsák I, Gulyás A, et al. A new method based on the use of diethyl pyrocarbonate as a nuclease inhibitor for the extraction of undegraded nucleic acid from plant tissues. Eur J Biochem 1968; 5: 520 – 527. | en_US |
dc.identifier.citedreference | Hallick RB, Chelm BK, Gray PW, et al. Use of aurintricarboxylic acid as an inhibitor of nucleases during nucleic acid isolation. Nucleic Acids Res 1977; 4: 3055 – 3064. | en_US |
dc.identifier.citedreference | Scholz C, Wagner E. Therapeutic plasmid DNA versus siRNA delivery: common and different tasks for synthetic carriers. J Control Release 2012; 161: 554 – 565. | en_US |
dc.identifier.citedreference | Hess P, Cooper D. Impact of pharmacogenomics on the clinical laboratory. Mol Diagnosis 1999; 4: 289 – 298. | en_US |
dc.identifier.citedreference | Liu C, Zhang N. Nanoparticles in gene therapy principles, prospects, and challenges. Prog Mol Biol Transl Sci 2011; 104: 509 – 662. | en_US |
dc.identifier.citedreference | Lechardeur D, Lukas GL. Intracellular barriers to non‐viral gene transfer. Curr Gene Ther 2002; 2: 183 – 194. | en_US |
dc.identifier.citedreference | Smedt SCD, Demeester J, Hennink WE. Cationic polymer based gene delivery systems. Pharm Res 2000; 17: 113 – 126. | en_US |
dc.identifier.citedreference | Benns JM, Choi J‐S, Mahato RI, et al. pH‐sensitive cationic polymer gene delivery vehicle: N‐Ac‐poly(L‐histidine)‐graft‐poly(L‐lysine) comb shaped polymer. Bioconjug Chem 2000; 11: 637 – 645. | en_US |
dc.identifier.citedreference | Luo D, Saltzman WM. Synthetic DNA delivery systems. Nature Biotechnol 2000; 18: 33 – 37. | en_US |
dc.identifier.citedreference | Lungwitz U, Breunig M, Blunk T, et al. Polyethylenimine‐based non‐viral gene delivery systems. Eur J Pharm Biopharm 2005; 60: 247 – 266. | en_US |
dc.identifier.citedreference | Hong S, Rattan R, Majoros IJ, et al. The role of ganglioside GM1 in cellular internalization mechanisms of poly(amidoamine) dendrimers. Bioconjugate Chem 2009; 20: 1503 – 1513. | en_US |
dc.identifier.citedreference | Qi R, Mullen DG, James R, Baker J, et al. The mechanism of polyplexes internalization into cells: testing the GM1/caveolin‐1‐mediated lipid raft mediated endocytosis pathway. Mol Pharm 2010; 7: 267 – 279. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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